Release AbAssayBench v1.0.0

.gitattributes

@@ -58,3 +58,11 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+results/all_model_test_predictions/prophet_ab_holdout_predictions_all_models.csv filter=lfs diff=lfs merge=lfs -text
+results/all_model_test_predictions/random_split_test_predictions_all_models.csv filter=lfs diff=lfs merge=lfs -text
+results/all_model_test_predictions/sequence_cluster_split_test_predictions_all_models.csv filter=lfs diff=lfs merge=lfs -text
+results/map_ab_figures/ablation/map_ab_ablation_main_figure.pdf filter=lfs diff=lfs merge=lfs -text
+results/map_ab_figures/ablation/map_ab_ablation_shap_combined.pdf filter=lfs diff=lfs merge=lfs -text
+results/map_ab_figures/ablation/map_ab_modality_shap.pdf filter=lfs diff=lfs merge=lfs -text
+splits/split_assignments.csv filter=lfs diff=lfs merge=lfs -text
+tables/flab2_measurements.csv filter=lfs diff=lfs merge=lfs -text

README.md

@@ -0,0 +1,100 @@
+---
+task_categories:
+- tabular-regression
+- feature-extraction
+tags:
+- antibody
+- antibody-developability
+- assay-metadata
+- multimodal-learning
+---
+
+# AbAssayBench
+
+This dataset repository contains the processed data package for **AbAssayBench**,
+a multi-endpoint antibody developability benchmark. The release combines the
+FLAb2.0-derived antibody measurements used for model development with the
+PROPHET-Ab measurements used for external validation.
+
+The repository is intended to be used together with the MAP-Ab source code:
+`https://github.com/gu-yaowen/MAP-Ab`.
+
+## Package layout
+
+| Path | Contents |
+| --- | --- |
+| `tables/` | Release tables with stable IDs and repository-relative file references. |
+| `assay_metadata/` | One JSON file per referenced assay metadata record. |
+| `structures/` | Antibody PDB files used by the processed structure features. |
+| `features/` | Precomputed sequence, structure, and assay-metadata feature stores. |
+| `splits/` | Long-format split assignments and split-size summaries. |
+| `results/` | Model predictions, endpoint metrics, tables, and publication figures. |
+| `schemas/` | Machine-readable description of the release contract. |
+| `manifests/` | Dataset, assay, structure, metadata, and file manifests. |
+
+## Main tables
+
+`tables/flab2_measurements.csv` and `tables/prophet_ab_measurements.csv` retain
+the measurement-level labels and canonical assay columns. Both tables add the
+following release identifiers:
+
+- `measurement_id`: stable identifier for one measurement row;
+- `antibody_id`: stable identifier for a heavy/light-chain pair;
+- `endpoint_id`: stable identifier for a property and endpoint definition;
+- `structure_id`: stable identifier for the source structure reference;
+- `assay_metadata_file`: path relative to this repository;
+- `structure_file`: path relative to this repository;
+- `property`: normalized broad property label;
+- `source_row_index`: original row index in the source table.
+
+The numeric measurement label is stored in the original `fitness` column.
+`value_definition` identifies the endpoint definition, while `assay_id`
+identifies the assay unit. The broad property labels are aggregation,
+expression, immunogenicity, pharmacokinetics, polyreactivity, and
+thermostability for the FLAb2.0-derived data; PROPHET-Ab retains its five
+benchmark property labels in the same schema.
+
+## Feature-store contract
+
+Each feature directory contains `features.npy`, `metadata.csv`, and, when
+available, `feature_info.json`. Row `i` in `features.npy` corresponds to row
+`i` in `metadata.csv`; `measurement_id` is the preferred join key. Feature
+arrays are stored as `float32` and are not re-normalized by this release.
+Directory names identify the feature family, including `esmc_600m`, `ism_3b`,
+`propermab_struct`, and the assay-metadata embedding stores.
+
+## Splits and results
+
+The split package is intentionally long-format: filter
+`splits/split_assignments.csv` by `split_family` and `replicate`, then join on
+`measurement_id`. The provided results are frozen outputs from the project
+analysis and are not required to reproduce the feature stores.
+
+## Downloading from Hugging Face
+
+Replace `<HF_USERNAME>` with the account or organization that owns the dataset
+repository:
+
+```bash
+hf download <HF_USERNAME>/AbAssayBench \
+  --repo-type dataset \
+  --local-dir ./AbAssayBench
+```
+
+## Loading example
+
+```python
+from pathlib import Path
+import numpy as np
+import pandas as pd
+
+root = Path("AbAssayBench")
+measurements = pd.read_parquet(root / "tables/flab2_measurements.parquet")
+feature_meta = pd.read_csv(root / "features/flab2/esmc_600m/metadata.csv")
+features = np.load(root / "features/flab2/esmc_600m/features.npy", mmap_mode="r")
+assert len(feature_meta) == features.shape[0]
+```
+
+The checksum file at `manifests/checksums.sha256` covers the release files.
+The source-attribution manifest records the component datasets and their roles;
+source redistribution conditions should be checked before public reuse.

VERSION

@@ -0,0 +1 @@
+1.0.0

assay_metadata/flab2/adams2017measuring_4420-fluorescein_exp_er_assay_metadata.txt

@@ -0,0 +1,74 @@
+{
+  "endpoint": "expression",
+  "assay_variants": [
+    {
+      "assay_name_reported": "Yeast surface display expression level (E)",
+      "assay_definition": "An indirect measure of the surface expression level of an scFv on yeast. Yeast cells displaying scFv variants with a C-terminal c-Myc tag are immunolabeled for the tag and sorted into multiple bins via FACS based on fluorescence intensity. The 'mean bin number' for each variant, calculated from its distribution across bins post-sequencing, serves as a proxy for its expression level.",
+      "readout": {
+        "primary_metric_name": "Expression Score (E)",
+        "raw_units": "Expression [ER]",
+        "normalized_units": "Enrichment ratio 4-4-20",
+        "directionality": "higher_is_better",
+        "value_transformations": "The primary readout is the 'mean bin number' calculated from FACS sorting based on expression level fluorescence. All E values are then scaled so that the mean of synonymous wild-type scFv variants is 1.0."
+      },
+      "sample_and_format": {
+        "molecule_format": "scFv (single-chain variable fragment)",
+        "concentration": "Not applicable (surface display)",
+        "buffer": "TBS-BSA (0.2 mg/ml BSA, 50 mM Tris, 25 mM NaCl, pH 8)",
+        "pH": "8",
+        "salt_or_additives": "25 mM NaCl",
+        "temperature": "Labeling performed at 4°C",
+        "incubation_or_stress": "Expression was induced for 16 hr at 20°C."
+      },
+      "antigen_info": {
+        "antigen_used": "false",
+        "binding_state": "unbound",
+        "notes": "Expression was quantified by immunolabeling a C-terminal c-Myc tag on the scFv construct."
+      },
+      "platform_and_instrumentation": {
+        "platform": "Yeast Surface Display with FACS",
+        "instrument_vendor_model": "Not specified",
+        "columns_or_chips_or_surfaces": "Yeast cells (strain EBY100)",
+        "detection_mode": "Fluorescence (Brilliant Violet 421)"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Yeast cells are labeled with a primary anti-c-Myc antibody and a BV421-conjugated secondary antibody, then sorted into bins via FACS based on BV421 signal. DNA from each bin is sequenced.",
+        "controls_and_standards": "The expression (E) values are scaled such that the mean of all synonymous wild-type (WT) variants is 1.0.",
+        "qc_criteria": "Yeast containing improperly cloned scFvs were filtered out by inducing expression and using FACS to recover cells positive for both HA and c-Myc epitopes.",
+        "reported_thresholds_or_bins": "No specific pass/fail threshold for expression is defined."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Three independent replicate Tite-Seq experiments were performed.",
+        "error_bars": "Not specified for expression values themselves, but correlations between replicates are reported for affinity values.",
+        "stat_tests": "Levene's test was used to compare the variance in expression effects between CDR1H and CDR3H regions."
+      },
+      "notes_on_ambiguity": [
+        "The specific FACS instrument model is not mentioned.",
+        "The 'Enrichment ratio 4-4-20' unit provided in the prompt is a misnomer for this assay; the paper describes a normalized expression score 'E' based on mean bin number, not a simple enrichment ratio. The 4-4-20 antibody is the template molecule."
+      ],
+      "evidence": [
+        {
+          "source_file": "elife-23156-v3.pdf",
+          "page": "9",
+          "location": "Low-throughput validation experiments",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "elife-23156-v3.pdf",
+          "page": "6",
+          "location": "Proof-of-principle Tite-Seq experiments",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "elife-23156-v3.pdf",
+          "page": "21",
+          "location": "Appendix 2, Yeast display",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "Expression assay: FACS instrument model"
+  ]
+}

assay_metadata/flab2/garbinski2023_exp_assay_metadata.txt

@@ -0,0 +1,54 @@
+{
+  "endpoint": "expression",
+  "assay_variants": [
+    {
+      "assay_name_reported": "",
+      "assay_definition": "",
+      "readout": {
+        "primary_metric_name": "",
+        "raw_units": "Expression (microg/mL)",
+        "normalized_units": "HEK",
+        "directionality": "not_specified",
+        "value_transformations": ""
+      },
+      "sample_and_format": {
+        "molecule_format": "",
+        "concentration": "",
+        "buffer": "",
+        "pH": "",
+        "salt_or_additives": "",
+        "temperature": "",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "",
+        "binding_state": "",
+        "notes": ""
+      },
+      "platform_and_instrumentation": {
+        "platform": "",
+        "instrument_vendor_model": "",
+        "columns_or_chips_or_surfaces": "",
+        "detection_mode": ""
+      },
+      "analysis_pipeline": {
+        "processing_steps": "",
+        "controls_and_standards": "",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": ""
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "The directory for this task only contains a 'readme.rtf' file stating 'In-house data from GlaxoSmithKline'. No primary manuscript or supplementary data files were available to search."
+      ],
+      "evidence": []
+    }
+  ],
+  "missing_fields_summary": [
+    "All fields are missing as no source documents containing experimental details were found in the specified directory."
+  ]
+}

assay_metadata/flab2/garbinski2023_tm1_assay_metadata.txt

@@ -0,0 +1,71 @@
+{
+  "endpoint": "thermostability",
+  "assay_variants": [
+    {
+      "assay_name_reported": "nanoDSF",
+      "assay_definition": "",
+      "readout": {
+        "primary_metric_name": "Tm1",
+        "raw_units": "Tm1 (nanoDSF)",
+        "normalized_units": "nanoDSF",
+        "directionality": "higher_is_better",
+        "value_transformations": ""
+      },
+      "sample_and_format": {
+        "molecule_format": "",
+        "concentration": "",
+        "buffer": "",
+        "pH": "",
+        "salt_or_additives": "",
+        "temperature": "",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "no antigen mentioned",
+        "binding_state": "",
+        "notes": ""
+      },
+      "platform_and_instrumentation": {
+        "platform": "nanoDSF",
+        "instrument_vendor_model": "",
+        "columns_or_chips_or_surfaces": "",
+        "detection_mode": ""
+      },
+      "analysis_pipeline": {
+        "processing_steps": "",
+        "controls_and_standards": "",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": ""
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "No specific information could be extracted from the provided file (readme.rtf) as it did not contain assay details. The JSON is populated only with the basic information provided in the prompt."
+      ],
+      "evidence": []
+    }
+  ],
+  "missing_fields_summary": [
+    "assay_definition",
+    "sample_and_format/molecule_format",
+    "sample_and_format/concentration",
+    "sample_and_format/buffer",
+    "sample_and_format/pH",
+    "sample_and_format/salt_or_additives",
+    "sample_and_format/temperature",
+    "sample_and_format/incubation_or_stress",
+    "platform_and_instrumentation/instrument_vendor_model",
+    "platform_and_instrumentation/columns_or_chips_or_surfaces",
+    "platform_and_instrumentation/detection_mode",
+    "analysis_pipeline/processing_steps",
+    "analysis_pipeline/controls_and_standards",
+    "analysis_pipeline/qc_criteria",
+    "analysis_pipeline/reported_thresholds_or_bins",
+    "replicates_and_statistics/n_replicates",
+    "replicates_and_statistics/error_bars",
+    "replicates_and_statistics/stat_tests"
+  ]
+}

assay_metadata/flab2/hie2023efficient_C143_Tm_assay_metadata.txt

@@ -0,0 +1,96 @@
+{
+  "endpoint": "thermostability",
+  "assay_variants": [
+    {
+      "assay_name_reported": "Differential Scanning Fluorimetry",
+      "assay_definition": "Measurement of the thermal unfolding of an antibody fragment by monitoring changes in intrinsic protein fluorescence (tryptophan fluorescence) as a function of temperature. The midpoint of the unfolding transition is reported as the melting temperature (Tm).",
+      "readout": {
+        "primary_metric_name": "Tm",
+        "raw_units": "Tm",
+        "normalized_units": "DSC",
+        "directionality": "higher_is_better",
+        "value_transformations": "The melting temperature (Tm) is determined from the peak of the first derivative of the ratio of intrinsic fluorescence at 350 nm / 330 nm."
+      },
+      "sample_and_format": {
+        "molecule_format": "Fab",
+        "concentration": "0.1 mg ml⁻¹",
+        "buffer": "",
+        "pH": "",
+        "salt_or_additives": "",
+        "temperature": "Temperature gradient from 20 °C to 95 °C at a heating rate of 1 °C per minute.",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "no antigen mentioned",
+        "binding_state": "",
+        "notes": "Thermostability was measured on the antibody fragment alone."
+      },
+      "platform_and_instrumentation": {
+        "platform": "nanoDSF",
+        "instrument_vendor_model": "Prometheus NT.48",
+        "columns_or_chips_or_surfaces": "glass capillaries",
+        "detection_mode": "Intrinsic fluorescence (350 nm and 330 nm)"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Melting temperatures were calculated automatically by the instrument software (PR.ThermControl version 2.3.1) from the peaks in the first derivative of the fluorescence ratio (350 nm/330 nm) vs. temperature plot.",
+        "controls_and_standards": "The wild-type version of each antibody (e.g., C143) serves as the reference control for its variants.",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": "A threshold of Tm > 70 °C is mentioned as maintaining thermostability for evolved variants."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "The prompt specified the assay unit as 'DSC', but the paper explicitly describes using Differential Scanning Fluorimetry (nanoDSF) on a Prometheus instrument. The extraction reflects the method described in the paper.",
+        "The buffer composition for the thermal melt samples is not explicitly stated in the methods section.",
+        "The number of replicates for the thermal melt measurements is not stated."
+      ],
+      "evidence": [
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "12",
+          "location": "Methods, Thermal melts",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "12",
+          "location": "Methods, Thermal melts",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "12",
+          "location": "Methods, Thermal melts",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "4",
+          "location": "Fig. 2c, C143 panel",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "3",
+          "location": "Left column, text under 'Additional characterization'",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "3",
+          "location": "Fig. 2 Legend",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "sample_and_format/buffer",
+    "sample_and_format/pH",
+    "sample_and_format/salt_or_additives",
+    "replicates_and_statistics/n_replicates"
+  ]
+}

assay_metadata/flab2/hie2023efficient_REGN10987_Tm_assay_metadata.txt

@@ -0,0 +1,96 @@
+{
+  "endpoint": "thermostability",
+  "assay_variants": [
+    {
+      "assay_name_reported": "Differential Scanning Fluorimetry",
+      "assay_definition": "Measurement of the thermal unfolding of an antibody fragment by monitoring changes in intrinsic protein fluorescence (tryptophan fluorescence) as a function of temperature. The midpoint of the unfolding transition is reported as the melting temperature (Tm).",
+      "readout": {
+        "primary_metric_name": "Tm",
+        "raw_units": "Tm",
+        "normalized_units": "DSC",
+        "directionality": "higher_is_better",
+        "value_transformations": "The melting temperature (Tm) is determined from the peak of the first derivative of the ratio of intrinsic fluorescence at 350 nm / 330 nm."
+      },
+      "sample_and_format": {
+        "molecule_format": "Fab",
+        "concentration": "0.1 mg ml⁻¹",
+        "buffer": "",
+        "pH": "",
+        "salt_or_additives": "",
+        "temperature": "Temperature gradient from 20 °C to 95 °C at a heating rate of 1 °C per minute.",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "no antigen mentioned",
+        "binding_state": "",
+        "notes": "Thermostability was measured on the antibody fragment alone."
+      },
+      "platform_and_instrumentation": {
+        "platform": "nanoDSF",
+        "instrument_vendor_model": "Prometheus NT.48",
+        "columns_or_chips_or_surfaces": "glass capillaries",
+        "detection_mode": "Intrinsic fluorescence (350 nm and 330 nm)"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Melting temperatures were calculated automatically by the instrument software (PR.ThermControl version 2.3.1) from the peaks in the first derivative of the fluorescence ratio (350 nm/330 nm) vs. temperature plot.",
+        "controls_and_standards": "The wild-type version of each antibody (e.g., REGN10987) serves as the reference control for its variants.",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": "A threshold of Tm > 70 °C is mentioned as maintaining thermostability for evolved variants."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "The prompt specified the assay unit as 'DSC', but the paper explicitly describes using Differential Scanning Fluorimetry (nanoDSF) on a Prometheus instrument. The extraction reflects the method described in the paper.",
+        "The buffer composition for the thermal melt samples is not explicitly stated in the methods section.",
+        "The number of replicates for the thermal melt measurements is not stated."
+      ],
+      "evidence": [
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "12",
+          "location": "Methods, Thermal melts",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "12",
+          "location": "Methods, Thermal melts",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "12",
+          "location": "Methods, Thermal melts",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "4",
+          "location": "Fig. 2c, REGN10987 panel",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "3",
+          "location": "Left column, text under 'Additional characterization'",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "3",
+          "location": "Fig. 2 Legend",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "sample_and_format/buffer",
+    "sample_and_format/pH",
+    "sample_and_format/salt_or_additives",
+    "replicates_and_statistics/n_replicates"
+  ]
+}

assay_metadata/flab2/hie2023efficient_S309_Tm_assay_metadata.txt

@@ -0,0 +1,102 @@
+{
+  "endpoint": "thermostability",
+  "assay_variants": [
+    {
+      "assay_name_reported": "Differential Scanning Fluorimetry",
+      "assay_definition": "Measurement of the thermal unfolding of an antibody fragment by monitoring changes in intrinsic protein fluorescence (tryptophan fluorescence) as a function of temperature. The midpoint of the unfolding transition is reported as the melting temperature (Tm).",
+      "readout": {
+        "primary_metric_name": "Tm",
+        "raw_units": "Tm",
+        "normalized_units": "DSC",
+        "directionality": "higher_is_better",
+        "value_transformations": "The melting temperature (Tm) is determined from the peak of the first derivative of the ratio of intrinsic fluorescence at 350 nm / 330 nm."
+      },
+      "sample_and_format": {
+        "molecule_format": "Fab",
+        "concentration": "0.1 mg ml⁻¹",
+        "buffer": "",
+        "pH": "",
+        "salt_or_additives": "",
+        "temperature": "Temperature gradient from 20 °C to 95 °C at a heating rate of 1 °C per minute.",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "no antigen mentioned",
+        "binding_state": "",
+        "notes": "Thermostability was measured on the antibody fragment alone."
+      },
+      "platform_and_instrumentation": {
+        "platform": "nanoDSF",
+        "instrument_vendor_model": "Prometheus NT.48",
+        "columns_or_chips_or_surfaces": "glass capillaries",
+        "detection_mode": "Intrinsic fluorescence (350 nm and 330 nm)"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Melting temperatures were calculated automatically by the instrument software (PR.ThermControl version 2.3.1) from the peaks in the first derivative of the fluorescence ratio (350 nm/330 nm) vs. temperature plot.",
+        "controls_and_standards": "The wild-type version of S309 serves as the reference control. Evolved S309 variants and a Sotrovimab variant are also discussed in the paper.",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": "A threshold of Tm > 70 °C is mentioned as maintaining thermostability for evolved variants. The paper also notes a specific Tm of 69.6 °C for the VH N55Q substitution in Sotrovimab."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "The prompt specified the assay unit as 'DSC', but the paper explicitly describes using Differential Scanning Fluorimetry (nanoDSF) on a Prometheus instrument. The extraction reflects the method described in the paper.",
+        "The buffer composition for the thermal melt samples is not explicitly stated in the methods section.",
+        "The number of replicates for the thermal melt measurements is not stated."
+      ],
+      "evidence": [
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "12",
+          "location": "Methods, Thermal melts",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "12",
+          "location": "Methods, Thermal melts",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "12",
+          "location": "Methods, Thermal melts",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "4",
+          "location": "Fig. 2c, S309 panel (wild-type)",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "4",
+          "location": "Main text, right column, first paragraph",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "3",
+          "location": "Left column, text under 'Additional characterization'",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "3",
+          "location": "Fig. 2 Legend",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "sample_and_format/buffer",
+    "sample_and_format/pH",
+    "sample_and_format/salt_or_additives",
+    "replicates_and_statistics/n_replicates"
+  ]
+}

assay_metadata/flab2/hie2023efficient_mAb114UCA_Tm_assay_metadata.txt

@@ -0,0 +1,96 @@
+{
+  "endpoint": "thermostability",
+  "assay_variants": [
+    {
+      "assay_name_reported": "Differential Scanning Fluorimetry",
+      "assay_definition": "Measurement of the thermal unfolding of an antibody fragment by monitoring changes in intrinsic protein fluorescence (tryptophan fluorescence) as a function of temperature. The midpoint of the unfolding transition is reported as the melting temperature (Tm).",
+      "readout": {
+        "primary_metric_name": "Tm",
+        "raw_units": "Tm",
+        "normalized_units": "DSC",
+        "directionality": "higher_is_better",
+        "value_transformations": "The melting temperature (Tm) is determined from the peak of the first derivative of the ratio of intrinsic fluorescence at 350 nm / 330 nm."
+      },
+      "sample_and_format": {
+        "molecule_format": "Fab",
+        "concentration": "0.1 mg ml⁻¹",
+        "buffer": "",
+        "pH": "",
+        "salt_or_additives": "",
+        "temperature": "Temperature gradient from 20 °C to 95 °C at a heating rate of 1 °C per minute.",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "no antigen mentioned",
+        "binding_state": "",
+        "notes": "Thermostability was measured on the antibody fragment alone."
+      },
+      "platform_and_instrumentation": {
+        "platform": "nanoDSF",
+        "instrument_vendor_model": "Prometheus NT.48",
+        "columns_or_chips_or_surfaces": "glass capillaries",
+        "detection_mode": "Intrinsic fluorescence (350 nm and 330 nm)"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Melting temperatures were calculated automatically by the instrument software (PR.ThermControl version 2.3.1) from the peaks in the first derivative of the fluorescence ratio (350 nm/330 nm) vs. temperature plot.",
+        "controls_and_standards": "The wild-type version of mAb114 UCA serves as the reference control for its variants.",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": "A threshold of Tm > 70 °C is mentioned as maintaining thermostability for evolved variants."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "The prompt specified the assay unit as 'DSC', but the paper explicitly describes using Differential Scanning Fluorimetry (nanoDSF) on a Prometheus instrument. The extraction reflects the method described in the paper.",
+        "The buffer composition for the thermal melt samples is not explicitly stated in the methods section.",
+        "The number of replicates for the thermal melt measurements is not stated."
+      ],
+      "evidence": [
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "12",
+          "location": "Methods, Thermal melts",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "12",
+          "location": "Methods, Thermal melts",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "12",
+          "location": "Methods, Thermal melts",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "4",
+          "location": "Fig. 2c, mAb114 UCA panel",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "3",
+          "location": "Left column, text under 'Additional characterization'",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "3",
+          "location": "Fig. 2 Legend",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "sample_and_format/buffer",
+    "sample_and_format/pH",
+    "sample_and_format/salt_or_additives",
+    "replicates_and_statistics/n_replicates"
+  ]
+}

assay_metadata/flab2/hie2023efficient_mAb114_Tm_assay_metadata.txt

@@ -0,0 +1,157 @@
+{
+  "endpoint": "thermostability",
+  "assay_variants": [
+    {
+      "assay_name_reported": "differential scanning fluorimetry",
+      "assay_definition": "Measurement of the melting temperature (Tm) of the Fab fragment, defined as the temperature at which the peak of the first derivative of the intrinsic fluorescence ratio (350 nm/330 nm) occurs during a thermal ramp. This assesses the point of thermal unfolding.",
+      "readout": {
+        "primary_metric_name": "Tm",
+        "raw_units": "°C",
+        "normalized_units": "DSC",
+        "directionality": "higher_is_better",
+        "value_transformations": "The primary metric is the absolute melting temperature (Tm). No transformations are mentioned."
+      },
+      "sample_and_format": {
+        "molecule_format": "Fab",
+        "concentration": "0.1 mg ml-1",
+        "buffer": "",
+        "pH": "",
+        "salt_or_additives": "",
+        "temperature": "Thermal ramp from 20 °C to 95 °C at a heating rate of 1 °C per minute.",
+        "incubation_or_stress": "Not specified"
+      },
+      "antigen_info": {
+        "antigen_used": "no",
+        "binding_state": "unbound",
+        "notes": "no antigen mentioned"
+      },
+      "platform_and_instrumentation": {
+        "platform": "nanoDSF (differential scanning fluorimetry)",
+        "instrument_vendor_model": "Prometheus NT.48",
+        "columns_or_chips_or_surfaces": "glass capillaries",
+        "detection_mode": "Intrinsic fluorescence ratio (350 nm / 330 nm)"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Melting temperatures are calculated as the peaks in the first derivative plot of the fluorescence ratio (350 nm/330 nm) versus temperature. The calculation is performed automatically by the instrument software.",
+        "controls_and_standards": "The wild-type version of mAb114 serves as the reference control for its variants.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "All tested variants were considered to have maintained thermostability, with Tm > 70 °C."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "The provided 'assay/units: DSC' (Differential Scanning Calorimetry) does not match the experimental platform, which is 'differential scanning fluorimetry' (a nanoDSF instrument). DSC measures heat capacity changes, while nanoDSF measures fluorescence changes. The reported metric is Tm in °C.",
+        "The buffer composition (including pH and salt/additives) for the final thermal melt measurement is not specified in the methods.",
+        "The number of replicates for the thermal melt measurements is not specified."
+      ],
+      "evidence": [
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "12",
+          "location": "Methods, Thermal melts",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "12",
+          "location": "Methods, Thermal melts",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "4",
+          "location": "Fig. 2b",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "3",
+          "location": "Results, Additional characterization of evolved antibodies",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "differential scanning fluorimetry",
+      "assay_definition": "Measurement of the melting temperature (Tm) of the Fab fragment, defined as the temperature at which the peak of the first derivative of the intrinsic fluorescence ratio (350 nm/330 nm) occurs during a thermal ramp. This assesses the point of thermal unfolding. This assay was performed on the unmutated common ancestor (UCA) of mAb114.",
+      "readout": {
+        "primary_metric_name": "Tm",
+        "raw_units": "°C",
+        "normalized_units": "DSC",
+        "directionality": "higher_is_better",
+        "value_transformations": "The primary metric is the absolute melting temperature (Tm). No transformations are mentioned."
+      },
+      "sample_and_format": {
+        "molecule_format": "Fab",
+        "concentration": "0.1 mg ml-1",
+        "buffer": "",
+        "pH": "",
+        "salt_or_additives": "",
+        "temperature": "Thermal ramp from 20 °C to 95 °C at a heating rate of 1 °C per minute.",
+        "incubation_or_stress": "Not specified"
+      },
+      "antigen_info": {
+        "antigen_used": "no",
+        "binding_state": "unbound",
+        "notes": "no antigen mentioned"
+      },
+      "platform_and_instrumentation": {
+        "platform": "nanoDSF (differential scanning fluorimetry)",
+        "instrument_vendor_model": "Prometheus NT.48",
+        "columns_or_chips_or_surfaces": "glass capillaries",
+        "detection_mode": "Intrinsic fluorescence ratio (350 nm / 330 nm)"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Melting temperatures are calculated as the peaks in the first derivative plot of the fluorescence ratio (350 nm/330 nm) versus temperature. The calculation is performed automatically by the instrument software.",
+        "controls_and_standards": "The wild-type version of mAb114 UCA serves as the reference control for its variants.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "All tested variants were considered to have maintained thermostability, with Tm > 70 °C."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "The provided 'assay/units: DSC' (Differential Scanning Calorimetry) does not match the experimental platform, which is 'differential scanning fluorimetry' (a nanoDSF instrument). DSC measures heat capacity changes, while nanoDSF measures fluorescence changes. The reported metric is Tm in °C.",
+        "The buffer composition (including pH and salt/additives) for the final thermal melt measurement is not specified in the methods.",
+        "The number of replicates for the thermal melt measurements is not specified."
+      ],
+      "evidence": [
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "12",
+          "location": "Methods, Thermal melts",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "12",
+          "location": "Methods, Thermal melts",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "4",
+          "location": "Fig. 2b",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "s41587-023-01763-2.pdf",
+          "page": "5",
+          "location": "Results",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "buffer",
+    "pH",
+    "salt_or_additives",
+    "n_replicates"
+  ]
+}

assay_metadata/flab2/hutchinson2023enhancement_multitm1_igg_assay_metadata.txt

@@ -0,0 +1,196 @@
+{
+  "endpoint": "thermostability",
+  "assay_variants": [
+    {
+      "assay_name_reported": "Tm1 by DSF",
+      "assay_definition": "The first melting temperature (Tm1) corresponding to the thermal unfolding of the IgG molecule, measured by differential scanning fluorimetry (DSF) using intrinsic tryptophan fluorescence.",
+      "readout": {
+        "primary_metric_name": "Tm1",
+        "raw_units": "Tm1 (degreeC) IgG",
+        "normalized_units": "DSC",
+        "directionality": "higher_is_better",
+        "value_transformations": "Tm1 is calculated from the baryricentric mean (BCM) of the intrinsic fluorescence intensity curve (300-450 nm) as a function of temperature."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "0.5-5 mg/mL",
+        "buffer": "PBS",
+        "pH": "7.2",
+        "salt_or_additives": "",
+        "temperature": "25-95°C",
+        "incubation_or_stress": "None mentioned"
+      },
+      "antigen_info": {
+        "antigen_used": "false",
+        "binding_state": "unbound",
+        "notes": "The paper explicitly states the design and measurement was performed in the absence of antigen."
+      },
+      "platform_and_instrumentation": {
+        "platform": "DSF (Differential Scanning Fluorimetry)",
+        "instrument_vendor_model": "Unchained Labs UNcle",
+        "columns_or_chips_or_surfaces": "UNcle UNI (quartz cuvette sample holder)",
+        "detection_mode": "Intrinsic tryptophan fluorescence (300-450 nm)"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Tm1 is determined from the barycentric mean (BCM) of the fluorescence intensity curves from 300 to 450 nm versus temperature, analyzed using the UNcle Analysis Software (V.6.0).",
+        "controls_and_standards": "Parental D44.1 antibody was used as a reference.",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": ""
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Duplicates",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "The exact buffer composition (PBS) and pH were inferred from the Fab fragmentation section, assuming the same buffer was used for the IgG analysis."
+      ],
+      "evidence": [
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "5",
+          "location": "Thermostability analysis",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "5",
+          "location": "Thermostability analysis",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "5",
+          "location": "Thermostability analysis",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "2",
+          "location": "Abstract",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "Tagg by SLS",
+      "assay_definition": "The aggregation temperature (Tagg) measured by static light scattering (SLS) during a thermal ramp.",
+      "readout": {
+        "primary_metric_name": "Tagg",
+        "raw_units": "Tm1 (degreeC) IgG",
+        "normalized_units": "DSC",
+        "directionality": "higher_is_better",
+        "value_transformations": "Tagg is determined from the intensity of light scattered at 266 nm as a function of temperature."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "0.5-5 mg/mL",
+        "buffer": "PBS",
+        "pH": "7.2",
+        "salt_or_additives": "",
+        "temperature": "25-95°C",
+        "incubation_or_stress": "None mentioned"
+      },
+      "antigen_info": {
+        "antigen_used": "false",
+        "binding_state": "unbound",
+        "notes": "The paper explicitly states the design and measurement was performed in the absence of antigen."
+      },
+      "platform_and_instrumentation": {
+        "platform": "SLS (Static Light Scattering)",
+        "instrument_vendor_model": "Unchained Labs UNcle",
+        "columns_or_chips_or_surfaces": "UNcle UNI (quartz cuvette sample holder)",
+        "detection_mode": "Static light scattering at 266 nm"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Tagg was determined from the intensity of light scattered at 266 nm. The exact calculation (e.g., onset threshold) is not specified.",
+        "controls_and_standards": "Parental D44.1 antibody was used as a reference.",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": ""
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Duplicates",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "The paper does not specify the exact algorithm or threshold used by the UNcle Analysis Software to calculate Tagg from the light scattering data."
+      ],
+      "evidence": [
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "5",
+          "location": "Thermostability analysis",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "5",
+          "location": "Thermostability analysis",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "Tonset by DSF",
+      "assay_definition": "The unfolding onset temperature (Tonset) measured by differential scanning fluorimetry (DSF) using intrinsic tryptophan fluorescence.",
+      "readout": {
+        "primary_metric_name": "Tonset",
+        "raw_units": "Tm1 (degreeC) IgG",
+        "normalized_units": "DSC",
+        "directionality": "higher_is_better",
+        "value_transformations": ""
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "0.5-5 mg/mL",
+        "buffer": "PBS",
+        "pH": "7.2",
+        "salt_or_additives": "",
+        "temperature": "25-95°C",
+        "incubation_or_stress": "None mentioned"
+      },
+      "antigen_info": {
+        "antigen_used": "false",
+        "binding_state": "unbound",
+        "notes": "The paper explicitly states the design and measurement was performed in the absence of antigen."
+      },
+      "platform_and_instrumentation": {
+        "platform": "DSF (Differential Scanning Fluorimetry)",
+        "instrument_vendor_model": "Unchained Labs UNcle",
+        "columns_or_chips_or_surfaces": "UNcle UNI (quartz cuvette sample holder)",
+        "detection_mode": "Intrinsic tryptophan fluorescence"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "The method for calculating Tonset is not explicitly defined in the paper, but it is reported as a result from the DSF experiment.",
+        "controls_and_standards": "Parental D44.1 antibody was used as a reference.",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": ""
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Duplicates",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "The paper reports Tonset values in Figure 3 but does not describe how Tonset is calculated from the raw fluorescence data in the methods section."
+      ],
+      "evidence": [
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "6",
+          "location": "Figure 3",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "salt_or_additives",
+    "incubation_or_stress",
+    "qc_criteria",
+    "reported_thresholds_or_bins",
+    "error_bars",
+    "stat_tests"
+  ]
+}

assay_metadata/flab2/hutchinson2023enhancement_singletm1_igg_assay_metadata.txt

@@ -0,0 +1,196 @@
+{
+  "endpoint": "thermostability",
+  "assay_variants": [
+    {
+      "assay_name_reported": "Tm1 by DSF",
+      "assay_definition": "The first melting temperature (Tm1) corresponding to the thermal unfolding of the IgG molecule, measured by differential scanning fluorimetry (DSF) using intrinsic tryptophan fluorescence.",
+      "readout": {
+        "primary_metric_name": "Tm1",
+        "raw_units": "Tm1 (degreeC) IgG",
+        "normalized_units": "DSC",
+        "directionality": "higher_is_better",
+        "value_transformations": "Tm1 is calculated from the barycentric mean (BCM) of the intrinsic fluorescence intensity curve (300-450 nm) as a function of temperature."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "0.5-5 mg/mL",
+        "buffer": "PBS",
+        "pH": "7.2",
+        "salt_or_additives": "",
+        "temperature": "25-95°C",
+        "incubation_or_stress": "None mentioned"
+      },
+      "antigen_info": {
+        "antigen_used": "false",
+        "binding_state": "unbound",
+        "notes": "The paper explicitly states the design and measurement was performed in the absence of antigen."
+      },
+      "platform_and_instrumentation": {
+        "platform": "DSF (Differential Scanning Fluorimetry)",
+        "instrument_vendor_model": "Unchained Labs UNcle",
+        "columns_or_chips_or_surfaces": "UNcle UNI (quartz cuvette sample holder)",
+        "detection_mode": "Intrinsic tryptophan fluorescence (300-450 nm)"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Tm1 is determined from the barycentric mean (BCM) of the fluorescence intensity curves from 300 to 450 nm versus temperature, analyzed using the UNcle Analysis Software (V.6.0).",
+        "controls_and_standards": "Parental D44.1 antibody was used as a reference.",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": ""
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Duplicates",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "The exact buffer composition (PBS) and pH were inferred from the Fab fragmentation section, assuming the same buffer was used for the IgG analysis."
+      ],
+      "evidence": [
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "5",
+          "location": "Thermostability analysis",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "5",
+          "location": "Thermostability analysis",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "5",
+          "location": "Thermostability analysis",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "2",
+          "location": "Abstract",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "Tagg by SLS",
+      "assay_definition": "The aggregation temperature (Tagg) measured by static light scattering (SLS) during a thermal ramp.",
+      "readout": {
+        "primary_metric_name": "Tagg",
+        "raw_units": "Tm1 (degreeC) IgG",
+        "normalized_units": "DSC",
+        "directionality": "higher_is_better",
+        "value_transformations": "Tagg is determined from the intensity of light scattered at 266 nm as a function of temperature."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "0.5-5 mg/mL",
+        "buffer": "PBS",
+        "pH": "7.2",
+        "salt_or_additives": "",
+        "temperature": "25-95°C",
+        "incubation_or_stress": "None mentioned"
+      },
+      "antigen_info": {
+        "antigen_used": "false",
+        "binding_state": "unbound",
+        "notes": "The paper explicitly states the design and measurement was performed in the absence of antigen."
+      },
+      "platform_and_instrumentation": {
+        "platform": "SLS (Static Light Scattering)",
+        "instrument_vendor_model": "Unchained Labs UNcle",
+        "columns_or_chips_or_surfaces": "UNcle UNI (quartz cuvette sample holder)",
+        "detection_mode": "Static light scattering at 266 nm"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Tagg was determined from the intensity of light scattered at 266 nm. The exact calculation (e.g., onset threshold) is not specified.",
+        "controls_and_standards": "Parental D44.1 antibody was used as a reference.",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": ""
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Duplicates",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "The paper does not specify the exact algorithm or threshold used by the UNcle Analysis Software to calculate Tagg from the light scattering data."
+      ],
+      "evidence": [
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "5",
+          "location": "Thermostability analysis",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "5",
+          "location": "Thermostability analysis",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "Tonset by DSF",
+      "assay_definition": "The unfolding onset temperature (Tonset) measured by differential scanning fluorimetry (DSF) using intrinsic tryptophan fluorescence.",
+      "readout": {
+        "primary_metric_name": "Tonset",
+        "raw_units": "Tm1 (degreeC) IgG",
+        "normalized_units": "DSC",
+        "directionality": "higher_is_better",
+        "value_transformations": ""
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "0.5-5 mg/mL",
+        "buffer": "PBS",
+        "pH": "7.2",
+        "salt_or_additives": "",
+        "temperature": "25-95°C",
+        "incubation_or_stress": "None mentioned"
+      },
+      "antigen_info": {
+        "antigen_used": "false",
+        "binding_state": "unbound",
+        "notes": "The paper explicitly states the design and measurement was performed in the absence of antigen."
+      },
+      "platform_and_instrumentation": {
+        "platform": "DSF (Differential Scanning Fluorimetry)",
+        "instrument_vendor_model": "Unchained Labs UNcle",
+        "columns_or_chips_or_surfaces": "UNcle UNI (quartz cuvette sample holder)",
+        "detection_mode": "Intrinsic tryptophan fluorescence"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "The method for calculating Tonset is not explicitly defined in the paper, but it is reported as a result from the DSF experiment.",
+        "controls_and_standards": "Parental D44.1 antibody was used as a reference.",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": ""
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Duplicates",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "The paper reports Tonset values in Figure 3 but does not describe how Tonset is calculated from the raw fluorescence data in the methods section."
+      ],
+      "evidence": [
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "6",
+          "location": "Figure 3",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "salt_or_additives",
+    "incubation_or_stress",
+    "qc_criteria",
+    "reported_thresholds_or_bins",
+    "error_bars",
+    "stat_tests"
+  ]
+}

assay_metadata/flab2/hutchinson2023enhancement_top200tm1_igg_assay_metadata.txt

@@ -0,0 +1,196 @@
+{
+  "endpoint": "thermostability",
+  "assay_variants": [
+    {
+      "assay_name_reported": "Tm1 by DSF",
+      "assay_definition": "The first melting temperature (Tm1) corresponding to the thermal unfolding of the IgG molecule, measured by differential scanning fluorimetry (DSF) using intrinsic tryptophan fluorescence.",
+      "readout": {
+        "primary_metric_name": "Tm1",
+        "raw_units": "Tm1 (degreeC) IgG",
+        "normalized_units": "DSC",
+        "directionality": "higher_is_better",
+        "value_transformations": "Tm1 is calculated from the barycentric mean (BCM) of the intrinsic fluorescence intensity curve (300-450 nm) as a function of temperature."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "0.5-5 mg/mL",
+        "buffer": "PBS",
+        "pH": "7.2",
+        "salt_or_additives": "",
+        "temperature": "25-95°C",
+        "incubation_or_stress": "None mentioned"
+      },
+      "antigen_info": {
+        "antigen_used": "false",
+        "binding_state": "unbound",
+        "notes": "The paper explicitly states the design and measurement was performed in the absence of antigen."
+      },
+      "platform_and_instrumentation": {
+        "platform": "DSF (Differential Scanning Fluorimetry)",
+        "instrument_vendor_model": "Unchained Labs UNcle",
+        "columns_or_chips_or_surfaces": "UNcle UNI (quartz cuvette sample holder)",
+        "detection_mode": "Intrinsic tryptophan fluorescence (300-450 nm)"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Tm1 is determined from the barycentric mean (BCM) of the fluorescence intensity curves from 300 to 450 nm versus temperature, analyzed using the UNcle Analysis Software (V.6.0).",
+        "controls_and_standards": "Parental D44.1 antibody was used as a reference.",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": ""
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Duplicates",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "The exact buffer composition (PBS) and pH were inferred from the Fab fragmentation section, assuming the same buffer was used for the IgG analysis."
+      ],
+      "evidence": [
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "5",
+          "location": "Thermostability analysis",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "5",
+          "location": "Thermostability analysis",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "5",
+          "location": "Thermostability analysis",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "2",
+          "location": "Abstract",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "Tagg by SLS",
+      "assay_definition": "The aggregation temperature (Tagg) measured by static light scattering (SLS) during a thermal ramp.",
+      "readout": {
+        "primary_metric_name": "Tagg",
+        "raw_units": "Tm1 (degreeC) IgG",
+        "normalized_units": "DSC",
+        "directionality": "higher_is_better",
+        "value_transformations": "Tagg is determined from the intensity of light scattered at 266 nm as a function of temperature."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "0.5-5 mg/mL",
+        "buffer": "PBS",
+        "pH": "7.2",
+        "salt_or_additives": "",
+        "temperature": "25-95°C",
+        "incubation_or_stress": "None mentioned"
+      },
+      "antigen_info": {
+        "antigen_used": "false",
+        "binding_state": "unbound",
+        "notes": "The paper explicitly states the design and measurement was performed in the absence of antigen."
+      },
+      "platform_and_instrumentation": {
+        "platform": "SLS (Static Light Scattering)",
+        "instrument_vendor_model": "Unchained Labs UNcle",
+        "columns_or_chips_or_surfaces": "UNcle UNI (quartz cuvette sample holder)",
+        "detection_mode": "Static light scattering at 266 nm"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Tagg was determined from the intensity of light scattered at 266 nm. The exact calculation (e.g., onset threshold) is not specified.",
+        "controls_and_standards": "Parental D44.1 antibody was used as a reference.",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": ""
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Duplicates",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "The paper does not specify the exact algorithm or threshold used by the UNcle Analysis Software to calculate Tagg from the light scattering data."
+      ],
+      "evidence": [
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "5",
+          "location": "Thermostability analysis",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "5",
+          "location": "Thermostability analysis",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "Tonset by DSF",
+      "assay_definition": "The unfolding onset temperature (Tonset) measured by differential scanning fluorimetry (DSF) using intrinsic tryptophan fluorescence.",
+      "readout": {
+        "primary_metric_name": "Tonset",
+        "raw_units": "Tm1 (degreeC) IgG",
+        "normalized_units": "DSC",
+        "directionality": "higher_is_better",
+        "value_transformations": ""
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "0.5-5 mg/mL",
+        "buffer": "PBS",
+        "pH": "7.2",
+        "salt_or_additives": "",
+        "temperature": "25-95°C",
+        "incubation_or_stress": "None mentioned"
+      },
+      "antigen_info": {
+        "antigen_used": "false",
+        "binding_state": "unbound",
+        "notes": "The paper explicitly states the design and measurement was performed in the absence of antigen."
+      },
+      "platform_and_instrumentation": {
+        "platform": "DSF (Differential Scanning Fluorimetry)",
+        "instrument_vendor_model": "Unchained Labs UNcle",
+        "columns_or_chips_or_surfaces": "UNcle UNI (quartz cuvette sample holder)",
+        "detection_mode": "Intrinsic tryptophan fluorescence"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "The method for calculating Tonset is not explicitly defined in the paper, but it is reported as a result from the DSF experiment.",
+        "controls_and_standards": "Parental D44.1 antibody was used as a reference.",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": ""
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Duplicates",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "The paper reports Tonset values in Figure 3 but does not describe how Tonset is calculated from the raw fluorescence data in the methods section."
+      ],
+      "evidence": [
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "6",
+          "location": "Figure 3",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "salt_or_additives",
+    "incubation_or_stress",
+    "qc_criteria",
+    "reported_thresholds_or_bins",
+    "error_bars",
+    "stat_tests"
+  ]
+}

assay_metadata/flab2/hutchinson2023enhancement_top27tm1_igg_assay_metadata.txt

@@ -0,0 +1,194 @@
+{
+  "endpoint": "thermostability",
+  "assay_variants": [
+    {
+      "assay_name_reported": "Tm1",
+      "assay_definition": "First melting temperature (Tm1) determined by intrinsic tryptophan fluorescence as a measure of thermal stability.",
+      "readout": {
+        "primary_metric_name": "Tm1",
+        "raw_units": "Tm1 (degreeC) IgG",
+        "normalized_units": "DSC",
+        "directionality": "higher_is_better",
+        "value_transformations": ""
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG",
+        "concentration": "0.5-5 mg/mL",
+        "buffer": "Purified antibodies in PBS, pH 7.2 (based on preceding purification steps, but not explicitly stated for this assay)",
+        "pH": "7.2 (inferred from purification buffer)",
+        "salt_or_additives": "",
+        "temperature": "Linear ramp from 25 to 95°C",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "no antigen mentioned",
+        "binding_state": "free",
+        "notes": "Thermostability was measured on the antibody alone."
+      },
+      "platform_and_instrumentation": {
+        "platform": "DSF (Differential Scanning Fluorimetry)",
+        "instrument_vendor_model": "UNcle system (Unchained Labs, CA, USA)",
+        "columns_or_chips_or_surfaces": "UNcle UNI (16 quartz cells)",
+        "detection_mode": "Intrinsic tryptophan fluorescence (excitation at 266 nm, emission spectrum 300-450 nm)"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "A linear temperature scan was applied at a rate of 1°C/min.",
+        "controls_and_standards": "",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": ""
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "duplicates",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "The exact buffer used for the thermostability measurement is not specified, it is inferred from the final purification steps.",
+        "The software version used for analysis is V.6.0, but further details on the barycentric mean (BCM) calculation are not provided."
+      ],
+      "evidence": [
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "6",
+          "location": "Section: \"Top 200\" designed variants exhibit greater thermostability and affinity",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "14",
+          "location": "Section: Thermostability analysis",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "Tonset",
+      "assay_definition": "Unfolding onset temperature (Tonset), measured as part of the thermal stability profile.",
+      "readout": {
+        "primary_metric_name": "Tonset",
+        "raw_units": "°C",
+        "normalized_units": "",
+        "directionality": "higher_is_better",
+        "value_transformations": ""
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG",
+        "concentration": "0.5-5 mg/mL",
+        "buffer": "Purified antibodies in PBS, pH 7.2 (based on preceding purification steps, but not explicitly stated for this assay)",
+        "pH": "7.2 (inferred from purification buffer)",
+        "salt_or_additives": "",
+        "temperature": "Linear ramp from 25 to 95°C",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "no antigen mentioned",
+        "binding_state": "free",
+        "notes": "Thermostability was measured on the antibody alone."
+      },
+      "platform_and_instrumentation": {
+        "platform": "DSF (Differential Scanning Fluorimetry)",
+        "instrument_vendor_model": "UNcle system (Unchained Labs, CA, USA)",
+        "columns_or_chips_or_surfaces": "UNcle UNI (16 quartz cells)",
+        "detection_mode": "Intrinsic tryptophan fluorescence (excitation at 266 nm)"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "A linear temperature scan was applied at a rate of 1°C/min.",
+        "controls_and_standards": "",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": ""
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "duplicates",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "The exact method for calculating Tonset from the fluorescence data is not specified in the main PDF. This detail may be in the inaccessible supplementary DOCX file.",
+        "The exact buffer used for the thermostability measurement is not specified."
+      ],
+      "evidence": [
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "6",
+          "location": "Section: \"Top 200\" designed variants exhibit greater thermostability and affinity",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "14",
+          "location": "Section: Thermostability analysis",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "Tagg",
+      "assay_definition": "Aggregation temperature (Tagg) determined by static light scattering (SLS) as a measure of colloidal stability under thermal stress.",
+      "readout": {
+        "primary_metric_name": "Tagg",
+        "raw_units": "°C",
+        "normalized_units": "",
+        "directionality": "higher_is_better",
+        "value_transformations": ""
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG",
+        "concentration": "0.5-5 mg/mL",
+        "buffer": "Purified antibodies in PBS, pH 7.2 (based on preceding purification steps, but not explicitly stated for this assay)",
+        "pH": "7.2 (inferred from purification buffer)",
+        "salt_or_additives": "",
+        "temperature": "Linear ramp from 25 to 95°C",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "no antigen mentioned",
+        "binding_state": "free",
+        "notes": "Thermostability was measured on the antibody alone."
+      },
+      "platform_and_instrumentation": {
+        "platform": "SLS (Static Light Scattering)",
+        "instrument_vendor_model": "UNcle system (Unchained Labs, CA, USA)",
+        "columns_or_chips_or_surfaces": "UNcle UNI (16 quartz cells)",
+        "detection_mode": "Light scattering at 266 nm"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "A linear temperature scan was applied at a rate of 1°C/min.",
+        "controls_and_standards": "",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": ""
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "duplicates",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "The exact buffer used for the thermostability measurement is not specified.",
+        "The software version used for analysis is V.6.0, but specific details of the Tagg calculation from light scattering intensity are not provided."
+      ],
+      "evidence": [
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "6",
+          "location": "Section: \"Top 200\" designed variants exhibit greater thermostability and affinity",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen.pdf",
+          "page": "14",
+          "location": "Section: Thermostability analysis",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "Contents of the supplementary DOCX file (kmab_a_2362775_sm3513.docx) could not be accessed.",
+    "Exact buffer composition for the thermostability analysis.",
+    "Explicit calculation method for Tonset.",
+    "Detailed parameters for the barycentric mean (BCM) calculation for Tm.",
+    "Detailed parameters for the Tagg calculation from light scattering intensity.",
+    "Information on control samples or standards used in the assays.",
+    "Specific QC criteria for the UNcle runs."
+  ]
+}

assay_metadata/flab2/jain2017biophyscial_HICRT_assay_metadata.txt

@@ -0,0 +1,99 @@
+{
+  "endpoint": "self-aggregation",
+  "assay_variants": [
+    {
+      "assay_name_reported": "Hydrophobic Interaction Chromatography (HIC)",
+      "assay_definition": "The assay measures the retention time of an antibody on a hydrophobic column under high salt conditions. This retention time is a measure of surface hydrophobicity and is used as an indicator of salt-induced aggregation propensity.",
+      "readout": {
+        "primary_metric_name": "Retention Time",
+        "raw_units": "HIC Retention Time (Min)a",
+        "normalized_units": "HIC",
+        "directionality": "lower_is_better",
+        "value_transformations": "The raw retention time in minutes is used directly. No transformations are mentioned."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "1 mg/mL",
+        "buffer": "Samples were diluted to 1 mg/mL in 20 mM His, pH 6.0 and then spiked into mobile phase A to achieve a final ammonium sulfate concentration of ~1 M.",
+        "pH": "6.0 (sample) / 6.5 (mobile phase)",
+        "salt_or_additives": "Mobile phase A: 1.8 M ammonium sulfate, 0.1 M sodium phosphate, pH 6.5. Mobile phase B: 0.1 M sodium phosphate, pH 6.5.",
+        "temperature": "Not specified",
+        "incubation_or_stress": "None mentioned beyond exposure to high salt mobile phase during the chromatography run."
+      },
+      "antigen_info": {
+        "antigen_used": "No",
+        "binding_state": "Unbound",
+        "notes": "No antigen was mentioned. The assay is performed on the antibody alone to assess its intrinsic properties."
+      },
+      "platform_and_instrumentation": {
+        "platform": "HIC-HPLC",
+        "instrument_vendor_model": "Agilent 1100 series HPLC (inferred from CIC method)",
+        "columns_or_chips_or_surfaces": "Sepax Proteomix HIC butyl-NP5 column",
+        "detection_mode": "UV absorbance at 280 nm"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "A linear gradient from mobile phase A to B was run over 20 minutes. The retention time of the main peak was recorded.",
+        "controls_and_standards": "Not specified",
+        "qc_criteria": "Not specified",
+        "reported_thresholds_or_bins": "A 'warning flag' is assigned for HIC retention time > 11.7 min, based on the 'worst 10% threshold' of 48 approved antibodies."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "The instrument model (Agilent 1100) is inferred from the description of the CIC assay in the same paper, but not explicitly stated for the HIC assay.",
+        "The number of replicates for HIC measurements is not specified in the main paper or supplementary information.",
+        "The temperature for the column or sample during the HIC analysis is not specified.",
+        "There is a discrepancy in sample preparation between the main paper (diluted in 20 mM His, pH 6.0) and the SI (spiked with mobile phase A, pH 6.5). The final JSON reflects a combination of these steps."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "Supporting Information, Materials and Methods, HIC",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "Supporting Information, Materials and Methods, HIC",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "Supporting Information, Materials and Methods, HIC",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "6",
+          "location": "Materials and Methods, Antibody Expression, Production, and Purification",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "2",
+          "location": "Brief Description of Assays",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "temperature",
+    "n_replicates",
+    "error_bars",
+    "stat_tests",
+    "controls_and_standards",
+    "qc_criteria"
+  ]
+}

assay_metadata/flab2/jain2017biophysical_ACSINS_assay_metadata.txt

@@ -0,0 +1,137 @@
+{
+  "endpoint": "self-aggregation",
+  "assay_variants": [
+    {
+      "assay_name_reported": "AC-SINS (Affinity-Capture Self-Interaction Nanoparticle Spectroscopy)",
+      "assay_definition": "Measures antibody self-interaction via wavelength shifts of antibody-coated gold nanoparticles. Increased self-interaction leads to particle agglomeration and a corresponding shift in the plasmon wavelength.",
+      "readout": {
+        "primary_metric_name": "Wavelength shift",
+        "raw_units": "Affinity-Capture Self-Interaction Nanoparticle Spectroscopy (AC-SINS) delta lambda max (nm) Average",
+        "normalized_units": "ACSINS",
+        "directionality": "lower_is_better",
+        "value_transformations": "The final readout is the measured wavelength shift in nanometers. No complex transformations are mentioned."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "Not specified",
+        "buffer": "Antibodies were buffer-exchanged into 25 mM Hepes, 150 mM sodium chloride, pH 7.3 prior to the assay. The assay itself seems to use PBS as the final sample buffer.",
+        "pH": "7.3",
+        "salt_or_additives": "150 mM sodium chloride",
+        "temperature": "Not specified (Assumed room temperature)",
+        "incubation_or_stress": "Incubated with gold nanoparticles for 2 hours."
+      },
+      "antigen_info": {
+        "antigen_used": "false",
+        "binding_state": "unbound",
+        "notes": "no antigen mentioned"
+      },
+      "platform_and_instrumentation": {
+        "platform": "Nanoparticle Spectroscopy",
+        "instrument_vendor_model": "Molecular Devices SpectraMax M2",
+        "columns_or_chips_or_surfaces": "Gold nanoparticles (Ted Pella Inc.) coated with anti-human IgG Fc (Jackson ImmunoResearch) and a non-specific polyclonal antibody.",
+        "detection_mode": "Plasmon wavelength absorbance"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "The wavelength shift for each antibody was measured and compared against a PBS control sample. A higher shift indicates greater self-interaction.",
+        "controls_and_standards": "A PBS sample is used as a baseline reference.",
+        "qc_criteria": "Not specified",
+        "reported_thresholds_or_bins": "The 'Worst 10% threshold' for approved antibodies was determined to be 11.8 +/- 6.2 nm. Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "The error for the threshold (±6.2 nm) is reported as a standard deviation based on bootstrapping.",
+        "stat_tests": "Fisher's exact test and Anderson-Darling test were used to compare distributions between clinical phases."
+      },
+      "notes_on_ambiguity": [
+        "The exact antibody concentration used in the AC-SINS incubation step is not specified.",
+        "The temperature for the 2-hour incubation in the AC-SINS assay is not specified."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "AC-SINS",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "6",
+          "location": "Materials and Methods",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "Accelerated Stability by SEC (AS SEC Slope)",
+      "assay_definition": "Measures the rate of aggregation by quantifying the loss of monomer over time during thermal stress. The slope of monomer loss versus time is calculated.",
+      "readout": {
+        "primary_metric_name": "Monomer percentage loss per day",
+        "raw_units": "Monomer percentage loss per day",
+        "normalized_units": "",
+        "directionality": "lower_is_better",
+        "value_transformations": "A linear slope is calculated from the percentage of aggregated species at different time points (days 0, 5, 20, 30)."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "1 mg/mL",
+        "buffer": "HBS (25 mM Hepes and 150 mM sodium chloride, pH 7.3)",
+        "pH": "7.3",
+        "salt_or_additives": "150 mM sodium chloride",
+        "temperature": "40 °C",
+        "incubation_or_stress": "Samples were incubated at 40°C for 30 days."
+      },
+      "antigen_info": {
+        "antigen_used": "false",
+        "binding_state": "unbound",
+        "notes": "no antigen mentioned"
+      },
+      "platform_and_instrumentation": {
+        "platform": "Size-Exclusion Chromatography (SEC)",
+        "instrument_vendor_model": "Inferred to be Agilent 1100 series HPLC system",
+        "columns_or_chips_or_surfaces": "SEC Column (0022855; Tosoh Bioscience)",
+        "detection_mode": "Not specified, likely UV absorbance."
+      },
+      "analysis_pipeline": {
+        "processing_steps": "A long-term stability slope was calculated from the percent aggregated, measured on the SEC at time points 0, 5, 20, and 30 days.",
+        "controls_and_standards": "Not specified, but day 0 serves as the baseline.",
+        "qc_criteria": "Not specified",
+        "reported_thresholds_or_bins": "The 'Worst 10% threshold' for approved antibodies was determined to be 0.08 +/- 0.03 % monomer loss per day."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "The error for the threshold (±0.03) is reported as a standard deviation based on bootstrapping.",
+        "stat_tests": "Not specified for this specific assay, but general statistical methods are described."
+      },
+      "notes_on_ambiguity": [
+        "The detection method for the SEC analysis is not explicitly stated but is typically UV absorbance.",
+        "The HPLC system model is inferred from descriptions of other chromatography-based assays in the paper."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "AS SEC Slope",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "AC-SINS: antibody concentration",
+    "AC-SINS: incubation temperature",
+    "AS-SEC: detection mode",
+    "AS-SEC: instrument_vendor_model (inferred)"
+  ]
+}

assay_metadata/flab2/jain2017biophysical_BVPELISA_assay_metadata.txt

@@ -0,0 +1,322 @@
+{
+  "endpoint": "polyreactivity",
+  "assay_variants": [
+    {
+      "assay_name_reported": "CIC",
+      "assay_definition": "Cross-Interaction Chromatography (CIC) measures the retention time of an antibody on a column where polyclonal human antibodies are immobilized. A longer retention time indicates a higher degree of undesirable cross-interaction with other antibodies.",
+      "readout": {
+        "primary_metric_name": "Retention time",
+        "raw_units": "min",
+        "normalized_units": "",
+        "directionality": "lower_is_better",
+        "value_transformations": "The raw retention time is used directly."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "~5 µg tested",
+        "buffer": "PBS was used as the mobile phase.",
+        "pH": "Not specified, likely ~7.4 for PBS.",
+        "salt_or_additives": "",
+        "temperature": "Not specified",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "Human serum polyclonal antibodies",
+        "binding_state": "Immobilized on a HiTrap column.",
+        "notes": "The polyclonal antibodies represent a diverse set of potential interaction partners."
+      },
+      "platform_and_instrumentation": {
+        "platform": "HPLC",
+        "instrument_vendor_model": "Agilent 1100 series HPLC system",
+        "columns_or_chips_or_surfaces": "1-mL HiTrap column (17-0716-01; GE Healthcare) coupled with ~30 mg of polyclonal antibodies (I4506; Sigma).",
+        "detection_mode": "Not specified, but typical for HPLC is UV absorbance."
+      },
+      "analysis_pipeline": {
+        "processing_steps": "The retention time of the major peak was assigned as the result.",
+        "controls_and_standards": "Not specified.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 10.1 ± 0.5 min. Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "The pH of the PBS mobile phase is not explicitly stated.",
+        "The detection method (e.g., UV wavelength) is not specified.",
+        "Details on controls and standards are not provided."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "CIC",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "PSR Binding Assay",
+      "assay_definition": "A flow cytometry-based assay measuring the binding of yeast-displayed antibodies to a biotinylated polyspecificity reagent (PSR) derived from soluble CHO cell membrane proteins. Higher fluorescence indicates more nonspecific binding.",
+      "readout": {
+        "primary_metric_name": "Normalized Median Fluorescence Intensity (MFI)",
+        "raw_units": "MFI in R-PE channel",
+        "normalized_units": "Normalized score (0 to 1)",
+        "directionality": "lower_is_better",
+        "value_transformations": "MFI values were normalized from 0 to 1 based on three reference antibodies exhibiting low, medium, and high PSR MFI values."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG-presenting yeast",
+        "concentration": "Not specified",
+        "buffer": "Not specified",
+        "pH": "Not specified",
+        "salt_or_additives": "Secondary labeling mix included Extravidin-R-PE, anti-human LC-FITC, and propidium iodide.",
+        "temperature": "Not specified",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "Polyspecificity Reagent (PSR)",
+        "binding_state": "Soluble, biotinylated membrane proteins prepared from CHO cells.",
+        "notes": "The enriched membrane fraction was biotinylated using NHS-LC-Biotin."
+      },
+      "platform_and_instrumentation": {
+        "platform": "Flow Cytometry",
+        "instrument_vendor_model": "FACSCanto (BD Biosciences) using an HTS sample injector",
+        "columns_or_chips_or_surfaces": "",
+        "detection_mode": "Fluorescence (R-PE channel for nonspecific binding)."
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Flow cytometry data were analyzed for median fluorescence intensity (MFI) in the R-PE channel to assess nonspecific binding.",
+        "controls_and_standards": "Three reference antibodies exhibiting low, medium, and high PSR MFI values were used for normalization.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 0.27 ± 0.06 (no units provided for normalized score). Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "The exact composition and preparation of the yeast-displayed IgG is not detailed in the SI.",
+        "Buffer compositions for incubation and washing are not specified."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "PSR Binding Assay",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "BVP Assay",
+      "assay_definition": "An ELISA-based assay that measures the binding of antibodies to immobilized baculovirus particles (BVP). A higher absorbance reading indicates greater nonspecific binding.",
+      "readout": {
+        "primary_metric_name": "BVP Score",
+        "raw_units": "Absorbance at 450 nm",
+        "normalized_units": "Fold-over-background",
+        "directionality": "lower_is_better",
+        "value_transformations": "BVP score was determined by normalizing the absorbance of the test antibody by the absorbance of control wells containing no test antibody."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "1 µM",
+        "buffer": "Blocking buffer: PBS with 0.5% BSA. Antibody dilution buffer is the same.",
+        "pH": "Coating buffer pH 9.6; blocking/assay buffer pH not specified, likely ~7.4 for PBS.",
+        "salt_or_additives": "Washes performed with PBS.",
+        "temperature": "Room temperature, except for overnight coating at 4 °C.",
+        "incubation_or_stress": "1 hour incubation with primary antibody."
+      },
+      "antigen_info": {
+        "antigen_used": "Baculovirus particles (BVP)",
+        "binding_state": "Immobilized on an ELISA plate overnight.",
+        "notes": "Source of BVP: BlueSky Biotech."
+      },
+      "platform_and_instrumentation": {
+        "platform": "ELISA",
+        "instrument_vendor_model": "Not specified, but plate absorbance reader.",
+        "columns_or_chips_or_surfaces": "Corning 3369 ELISA plates",
+        "detection_mode": "Absorbance at 450 nm after TMB substrate reaction."
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Reaction stopped with 2 M sulfuric acid. Absorbance read at 450 nm. Score calculated as fold-over-background.",
+        "controls_and_standards": "Control wells with no test antibody were used for background normalization.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 4.3 ± 2.2 Fold-over-background. Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "The instrument model for the plate reader is not specified.",
+        "The paper notes the analysis method (background being 'no antibody') differs from the original Hötzel et al. paper and may be 'over-stringent'."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "BVP Assay",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "2",
+          "location": "Further Details on the BVP Assay",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "ELISA",
+      "assay_definition": "A multi-antigen ELISA measuring antibody binding to a panel of six different nonspecific antigens: cardiolipin, KLH, LPS, ssDNA, dsDNA, and insulin.",
+      "readout": {
+        "primary_metric_name": "ELISA Score",
+        "raw_units": "Absorbance at 450 nm",
+        "normalized_units": "Fold-over-background",
+        "directionality": "lower_is_better",
+        "value_transformations": "The final reported value is a single 'Fold-over-background' score, implying a composite or averaged result from the six antigens."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "100 nM",
+        "buffer": "Blocking buffer: PBS with 0.5% BSA.",
+        "pH": "Not specified, likely ~7.4 for PBS.",
+        "salt_or_additives": "Washes performed with PBST (PBS plus 0.1% Tween 20).",
+        "temperature": "Room temperature, except for overnight coating at 4 °C.",
+        "incubation_or_stress": "1 hour incubation with antibody."
+      },
+      "antigen_info": {
+        "antigen_used": "Cardiolipin, Keyhole limpet hemocyanin (KLH), Lipopolysaccharide (LPS), single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), insulin.",
+        "binding_state": "Immobilized individually on ELISA plates.",
+        "notes": "All antigens sourced from Sigma or InvivoGen, catalog numbers provided."
+      },
+      "platform_and_instrumentation": {
+        "platform": "ELISA",
+        "instrument_vendor_model": "Not specified",
+        "columns_or_chips_or_surfaces": "Corning 3369 ELISA plates",
+        "detection_mode": "Absorbance at 450 nm"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Procedure follows the BVP assay after the coating step. The method for combining the readouts from the six antigens into a single score is not detailed.",
+        "controls_and_standards": "Not specified, but likely uses a 'no antibody' background control similar to the BVP assay.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 1.9 ± 1.0 Fold-over-background. Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "The method for calculating the single 'ELISA' score from the six different antigen wells is not described.",
+        "The instrument model for the plate reader is not specified."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "ELISA",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "HIC",
+      "assay_definition": "Hydrophobic Interaction Chromatography (HIC) measures the retention time of an antibody on a hydrophobic column under high salt conditions. It is a measure of surface hydrophobicity, which can correlate with nonspecific binding and poor developability. Longer retention time indicates greater hydrophobicity.",
+      "readout": {
+        "primary_metric_name": "Retention time",
+        "raw_units": "min",
+        "normalized_units": "",
+        "directionality": "lower_is_better",
+        "value_transformations": ""
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "5 µg (from 1 mg/mL stock)",
+        "buffer": "Mobile Phase A: 1.8 M ammonium sulfate and 0.1 M sodium phosphate. Mobile Phase B: 0.1 M sodium phosphate.",
+        "pH": "6.5",
+        "salt_or_additives": "Samples spiked with mobile phase A to a final ammonium sulfate concentration of ~1 M.",
+        "temperature": "Not specified",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "N/A (interaction is with a chemical surface)",
+        "binding_state": "N/A",
+        "notes": ""
+      },
+      "platform_and_instrumentation": {
+        "platform": "HPLC",
+        "instrument_vendor_model": "Not specified",
+        "columns_or_chips_or_surfaces": "Sepax Proteomix HIC butyl-NP5 column",
+        "detection_mode": "UV absorbance at 280 nm"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Analyzed with a linear gradient of mobile phase A to B over 20 min.",
+        "controls_and_standards": "Not specified.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 11.7 ± 0.6 min. Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "Although a measure of hydrophobicity, its inclusion as a 'polyreactivity' assay is interpretive, but it is a common developability assay that measures a related property.",
+        "The HPLC instrument vendor/model is not specified."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "HIC",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "replicates_and_statistics",
+    "qc_criteria",
+    "controls_and_standards",
+    "instrument_vendor_model (for ELISA and HIC)",
+    "temperature (for most assays)",
+    "n_replicates",
+    "error_bars",
+    "stat_tests"
+  ]
+}

assay_metadata/flab2/jain2017biophysical_CICRT_assay_metadata.txt

@@ -0,0 +1,322 @@
+{
+  "endpoint": "polyreactivity",
+  "assay_variants": [
+    {
+      "assay_name_reported": "CIC",
+      "assay_definition": "Cross-Interaction Chromatography (CIC) measures the retention time of an antibody on a column where polyclonal human antibodies are immobilized. A longer retention time indicates a higher degree of undesirable cross-interaction with other antibodies.",
+      "readout": {
+        "primary_metric_name": "Retention time",
+        "raw_units": "CIC Retention Time (Min)",
+        "normalized_units": "CIC",
+        "directionality": "lower_is_better",
+        "value_transformations": "The raw retention time is used directly."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "~5 µg tested",
+        "buffer": "PBS was used as the mobile phase.",
+        "pH": "Not specified, likely ~7.4 for PBS.",
+        "salt_or_additives": "",
+        "temperature": "Not specified",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "Human serum polyclonal antibodies",
+        "binding_state": "Immobilized on a HiTrap column.",
+        "notes": "The polyclonal antibodies represent a diverse set of potential interaction partners."
+      },
+      "platform_and_instrumentation": {
+        "platform": "HPLC",
+        "instrument_vendor_model": "Agilent 1100 series HPLC system",
+        "columns_or_chips_or_surfaces": "1-mL HiTrap column (17-0716-01; GE Healthcare) coupled with ~30 mg of polyclonal antibodies (I4506; Sigma).",
+        "detection_mode": "Not specified, but typical for HPLC is UV absorbance."
+      },
+      "analysis_pipeline": {
+        "processing_steps": "The retention time of the major peak was assigned as the result.",
+        "controls_and_standards": "Not specified.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 10.1 ± 0.5 min. Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "The pH of the PBS mobile phase is not explicitly stated.",
+        "The detection method (e.g., UV wavelength) is not specified.",
+        "Details on controls and standards are not provided."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "CIC",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "PSR Binding Assay",
+      "assay_definition": "A flow cytometry-based assay measuring the binding of yeast-displayed antibodies to a biotinylated polyspecificity reagent (PSR) derived from soluble CHO cell membrane proteins. Higher fluorescence indicates more nonspecific binding.",
+      "readout": {
+        "primary_metric_name": "Normalized Median Fluorescence Intensity (MFI)",
+        "raw_units": "MFI in R-PE channel",
+        "normalized_units": "Normalized score (0 to 1)",
+        "directionality": "lower_is_better",
+        "value_transformations": "MFI values were normalized from 0 to 1 based on three reference antibodies exhibiting low, medium, and high PSR MFI values."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG-presenting yeast",
+        "concentration": "Not specified",
+        "buffer": "Not specified",
+        "pH": "Not specified",
+        "salt_or_additives": "Secondary labeling mix included Extravidin-R-PE, anti-human LC-FITC, and propidium iodide.",
+        "temperature": "Not specified",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "Polyspecificity Reagent (PSR)",
+        "binding_state": "Soluble, biotinylated membrane proteins prepared from CHO cells.",
+        "notes": "The enriched membrane fraction was biotinylated using NHS-LC-Biotin."
+      },
+      "platform_and_instrumentation": {
+        "platform": "Flow Cytometry",
+        "instrument_vendor_model": "FACSCanto (BD Biosciences) using an HTS sample injector",
+        "columns_or_chips_or_surfaces": "",
+        "detection_mode": "Fluorescence (R-PE channel for nonspecific binding)."
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Flow cytometry data were analyzed for median fluorescence intensity (MFI) in the R-PE channel to assess nonspecific binding.",
+        "controls_and_standards": "Three reference antibodies exhibiting low, medium, and high PSR MFI values were used for normalization.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 0.27 ± 0.06 (no units provided for normalized score). Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "The exact composition and preparation of the yeast-displayed IgG is not detailed in the SI.",
+        "Buffer compositions for incubation and washing are not specified."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "PSR Binding Assay",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "BVP Assay",
+      "assay_definition": "An ELISA-based assay that measures the binding of antibodies to immobilized baculovirus particles (BVP). A higher absorbance reading indicates greater nonspecific binding.",
+      "readout": {
+        "primary_metric_name": "BVP Score",
+        "raw_units": "Absorbance at 450 nm",
+        "normalized_units": "Fold-over-background",
+        "directionality": "lower_is_better",
+        "value_transformations": "BVP score was determined by normalizing the absorbance of the test antibody by the absorbance of control wells containing no test antibody."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "1 µM",
+        "buffer": "Blocking buffer: PBS with 0.5% BSA. Antibody dilution buffer is the same.",
+        "pH": "Coating buffer pH 9.6; blocking/assay buffer pH not specified, likely ~7.4 for PBS.",
+        "salt_or_additives": "Washes performed with PBS.",
+        "temperature": "Room temperature, except for overnight coating at 4 °C.",
+        "incubation_or_stress": "1 hour incubation with primary antibody."
+      },
+      "antigen_info": {
+        "antigen_used": "Baculovirus particles (BVP)",
+        "binding_state": "Immobilized on an ELISA plate overnight.",
+        "notes": "Source of BVP: BlueSky Biotech."
+      },
+      "platform_and_instrumentation": {
+        "platform": "ELISA",
+        "instrument_vendor_model": "Not specified, but plate absorbance reader.",
+        "columns_or_chips_or_surfaces": "Corning 3369 ELISA plates",
+        "detection_mode": "Absorbance at 450 nm after TMB substrate reaction."
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Reaction stopped with 2 M sulfuric acid. Absorbance read at 450 nm. Score calculated as fold-over-background.",
+        "controls_and_standards": "Control wells with no test antibody were used for background normalization.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 4.3 ± 2.2 Fold-over-background. Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "The instrument model for the plate reader is not specified.",
+        "The paper notes the analysis method (background being 'no antibody') differs from the original Hötzel et al. paper and may be 'over-stringent'."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "BVP Assay",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "2",
+          "location": "Further Details on the BVP Assay",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "ELISA",
+      "assay_definition": "A multi-antigen ELISA measuring antibody binding to a panel of six different nonspecific antigens: cardiolipin, KLH, LPS, ssDNA, dsDNA, and insulin.",
+      "readout": {
+        "primary_metric_name": "ELISA Score",
+        "raw_units": "Absorbance at 450 nm",
+        "normalized_units": "Fold-over-background",
+        "directionality": "lower_is_better",
+        "value_transformations": "The final reported value is a single 'Fold-over-background' score, implying a composite or averaged result from the six antigens."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "100 nM",
+        "buffer": "Blocking buffer: PBS with 0.5% BSA.",
+        "pH": "Not specified, likely ~7.4 for PBS.",
+        "salt_or_additives": "Washes performed with PBST (PBS plus 0.1% Tween 20).",
+        "temperature": "Room temperature, except for overnight coating at 4 °C.",
+        "incubation_or_stress": "1 hour incubation with antibody."
+      },
+      "antigen_info": {
+        "antigen_used": "Cardiolipin, Keyhole limpet hemocyanin (KLH), Lipopolysaccharide (LPS), single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), insulin.",
+        "binding_state": "Immobilized individually on ELISA plates.",
+        "notes": "All antigens sourced from Sigma or InvivoGen, catalog numbers provided."
+      },
+      "platform_and_instrumentation": {
+        "platform": "ELISA",
+        "instrument_vendor_model": "Not specified",
+        "columns_or_chips_or_surfaces": "Corning 3369 ELISA plates",
+        "detection_mode": "Absorbance at 450 nm"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Procedure follows the BVP assay after the coating step. The method for combining the readouts from the six antigens into a single score is not detailed.",
+        "controls_and_standards": "Not specified, but likely uses a 'no antibody' background control similar to the BVP assay.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 1.9 ± 1.0 Fold-over-background. Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "The method for calculating the single 'ELISA' score from the six different antigen wells is not described.",
+        "The instrument model for the plate reader is not specified."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "ELISA",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "HIC",
+      "assay_definition": "Hydrophobic Interaction Chromatography (HIC) measures the retention time of an antibody on a hydrophobic column under high salt conditions. It is a measure of surface hydrophobicity, which can correlate with nonspecific binding and poor developability. Longer retention time indicates greater hydrophobicity.",
+      "readout": {
+        "primary_metric_name": "Retention time",
+        "raw_units": "min",
+        "normalized_units": "",
+        "directionality": "lower_is_better",
+        "value_transformations": ""
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "5 µg (from 1 mg/mL stock)",
+        "buffer": "Mobile Phase A: 1.8 M ammonium sulfate and 0.1 M sodium phosphate. Mobile Phase B: 0.1 M sodium phosphate.",
+        "pH": "6.5",
+        "salt_or_additives": "Samples spiked with mobile phase A to a final ammonium sulfate concentration of ~1 M.",
+        "temperature": "Not specified",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "N/A (interaction is with a chemical surface)",
+        "binding_state": "N/A",
+        "notes": ""
+      },
+      "platform_and_instrumentation": {
+        "platform": "HPLC",
+        "instrument_vendor_model": "Not specified",
+        "columns_or_chips_or_surfaces": "Sepax Proteomix HIC butyl-NP5 column",
+        "detection_mode": "UV absorbance at 280 nm"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Analyzed with a linear gradient of mobile phase A to B over 20 min.",
+        "controls_and_standards": "Not specified.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 11.7 ± 0.6 min. Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "Although a measure of hydrophobicity, its inclusion as a 'polyreactivity' assay is interpretive, but it is a common developability assay that measures a related property.",
+        "The HPLC instrument vendor/model is not specified."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "HIC",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "replicates_and_statistics",
+    "qc_criteria",
+    "controls_and_standards",
+    "instrument_vendor_model (for ELISA and HIC)",
+    "temperature (for most assays)",
+    "n_replicates",
+    "error_bars",
+    "stat_tests"
+  ]
+}

assay_metadata/flab2/jain2017biophysical_CSIBLI_assay_metadata.txt

@@ -0,0 +1,75 @@
+{
+  "endpoint": "self-aggregation",
+  "assay_variants": [
+    {
+      "assay_name_reported": "CSI-BLI (clone self-interaction by bio-layer interferometry)",
+      "assay_definition": "Measures antibody self-interaction by immobilizing an antibody on a biosensor and then measuring its binding to itself in solution. The binding response, a shift in light interference, is measured in nanometers.",
+      "readout": {
+        "primary_metric_name": "Delta Response",
+        "raw_units": "CSI-BLI Delta Response (nm)",
+        "normalized_units": "CSIBLI",
+        "directionality": "lower_is_better",
+        "value_transformations": "The raw binding response from the self-association step is normalized by subtracting the response of a reference IgG (adalimumab)."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "1 µM",
+        "buffer": "Assumed to be the general antibody buffer: 25 mM Hepes and 150 mM sodium chloride.",
+        "pH": "7.3",
+        "salt_or_additives": "150 mM sodium chloride",
+        "temperature": "Not specified (Assumed room temperature)",
+        "incubation_or_stress": "The self-association measurement was performed for 300 seconds."
+      },
+      "antigen_info": {
+        "antigen_used": "false",
+        "binding_state": "unbound",
+        "notes": "no antigen mentioned"
+      },
+      "platform_and_instrumentation": {
+        "platform": "Bio-layer Interferometry (BLI)",
+        "instrument_vendor_model": "Octet HTX system (ForteBio)",
+        "columns_or_chips_or_surfaces": "AHQ biosensor (ForteBio), blocked with human IgG1 Fc.",
+        "detection_mode": "Interferometry (wavelength shift)"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Human IgG is loaded onto the biosensor. Self-association is measured for 300s. The resulting binding response is subtracted from the response of a reference antibody (adalimumab) to get the final metric.",
+        "controls_and_standards": "A reference IgG (adalimumab) is used as a subtraction control. The sensor is blocked with human IgG1 Fc.",
+        "qc_criteria": "Not specified",
+        "reported_thresholds_or_bins": "The 'Worst 10% threshold' for approved antibodies was determined to be 0.01 +/- 0.02 BLI response units. Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "The error for the threshold (±0.02) is reported as a standard deviation based on bootstrapping.",
+        "stat_tests": "Fisher's exact test and Anderson-Darling test were used to compare distributions between clinical phases."
+      },
+      "notes_on_ambiguity": [
+        "The buffer used during the BLI measurement is not explicitly stated; it is assumed to be the standard antibody formulation buffer mentioned in the main text.",
+        "The temperature of the CSI-BLI measurement is not specified."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "CSI-BLI",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "2",
+          "location": "Brief Description of Assays",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "CSI-BLI: assay buffer (inferred)",
+    "CSI-BLI: assay temperature"
+  ]
+}

assay_metadata/flab2/jain2017biophysical_ELISA_assay_metadata.txt

@@ -0,0 +1,322 @@
+{
+  "endpoint": "polyreactivity",
+  "assay_variants": [
+    {
+      "assay_name_reported": "ELISA",
+      "assay_definition": "A multi-antigen ELISA measuring antibody binding to a panel of six different nonspecific antigens: cardiolipin, KLH, LPS, ssDNA, dsDNA, and insulin.",
+      "readout": {
+        "primary_metric_name": "ELISA Score",
+        "raw_units": "ELISA",
+        "normalized_units": "ELISA",
+        "directionality": "lower_is_better",
+        "value_transformations": "The final reported value is a single 'Fold-over-background' score, implying a composite or averaged result from the six antigens."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "100 nM",
+        "buffer": "Blocking buffer: PBS with 0.5% BSA.",
+        "pH": "Not specified, likely ~7.4 for PBS.",
+        "salt_or_additives": "Washes performed with PBST (PBS plus 0.1% Tween 20).",
+        "temperature": "Room temperature, except for overnight coating at 4 °C.",
+        "incubation_or_stress": "1 hour incubation with antibody."
+      },
+      "antigen_info": {
+        "antigen_used": "Cardiolipin, Keyhole limpet hemocyanin (KLH), Lipopolysaccharide (LPS), single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), insulin.",
+        "binding_state": "Immobilized individually on ELISA plates.",
+        "notes": "All antigens sourced from Sigma or InvivoGen, catalog numbers provided."
+      },
+      "platform_and_instrumentation": {
+        "platform": "ELISA",
+        "instrument_vendor_model": "Not specified",
+        "columns_or_chips_or_surfaces": "Corning 3369 ELISA plates",
+        "detection_mode": "Absorbance at 450 nm"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Procedure follows the BVP assay after the coating step. The method for combining the readouts from the six antigens into a single score is not detailed.",
+        "controls_and_standards": "Not specified, but likely uses a 'no antibody' background control similar to the BVP assay.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 1.9 ± 1.0 Fold-over-background. Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "The method for calculating the single 'ELISA' score from the six different antigen wells is not described.",
+        "The instrument model for the plate reader is not specified."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "ELISA",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "CIC",
+      "assay_definition": "Cross-Interaction Chromatography (CIC) measures the retention time of an antibody on a column where polyclonal human antibodies are immobilized. A longer retention time indicates a higher degree of undesirable cross-interaction with other antibodies.",
+      "readout": {
+        "primary_metric_name": "Retention time",
+        "raw_units": "min",
+        "normalized_units": "",
+        "directionality": "lower_is_better",
+        "value_transformations": "The raw retention time is used directly."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "~5 µg tested",
+        "buffer": "PBS was used as the mobile phase.",
+        "pH": "Not specified, likely ~7.4 for PBS.",
+        "salt_or_additives": "",
+        "temperature": "Not specified",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "Human serum polyclonal antibodies",
+        "binding_state": "Immobilized on a HiTrap column.",
+        "notes": "The polyclonal antibodies represent a diverse set of potential interaction partners."
+      },
+      "platform_and_instrumentation": {
+        "platform": "HPLC",
+        "instrument_vendor_model": "Agilent 1100 series HPLC system",
+        "columns_or_chips_or_surfaces": "1-mL HiTrap column (17-0716-01; GE Healthcare) coupled with ~30 mg of polyclonal antibodies (I4506; Sigma).",
+        "detection_mode": "Not specified, but typical for HPLC is UV absorbance."
+      },
+      "analysis_pipeline": {
+        "processing_steps": "The retention time of the major peak was assigned as the result.",
+        "controls_and_standards": "Not specified.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 10.1 ± 0.5 min. Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "The pH of the PBS mobile phase is not explicitly stated.",
+        "The detection method (e.g., UV wavelength) is not specified.",
+        "Details on controls and standards are not provided."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "CIC",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "PSR Binding Assay",
+      "assay_definition": "A flow cytometry-based assay measuring the binding of yeast-displayed antibodies to a biotinylated polyspecificity reagent (PSR) derived from soluble CHO cell membrane proteins. Higher fluorescence indicates more nonspecific binding.",
+      "readout": {
+        "primary_metric_name": "Normalized Median Fluorescence Intensity (MFI)",
+        "raw_units": "MFI in R-PE channel",
+        "normalized_units": "Normalized score (0 to 1)",
+        "directionality": "lower_is_better",
+        "value_transformations": "MFI values were normalized from 0 to 1 based on three reference antibodies exhibiting low, medium, and high PSR MFI values."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG-presenting yeast",
+        "concentration": "Not specified",
+        "buffer": "Not specified",
+        "pH": "Not specified",
+        "salt_or_additives": "Secondary labeling mix included Extravidin-R-PE, anti-human LC-FITC, and propidium iodide.",
+        "temperature": "Not specified",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "Polyspecificity Reagent (PSR)",
+        "binding_state": "Soluble, biotinylated membrane proteins prepared from CHO cells.",
+        "notes": "The enriched membrane fraction was biotinylated using NHS-LC-Biotin."
+      },
+      "platform_and_instrumentation": {
+        "platform": "Flow Cytometry",
+        "instrument_vendor_model": "FACSCanto (BD Biosciences) using an HTS sample injector",
+        "columns_or_chips_or_surfaces": "",
+        "detection_mode": "Fluorescence (R-PE channel for nonspecific binding)."
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Flow cytometry data were analyzed for median fluorescence intensity (MFI) in the R-PE channel to assess nonspecific binding.",
+        "controls_and_standards": "Three reference antibodies exhibiting low, medium, and high PSR MFI values were used for normalization.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 0.27 ± 0.06 (no units provided for normalized score). Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "The exact composition and preparation of the yeast-displayed IgG is not detailed in the SI.",
+        "Buffer compositions for incubation and washing are not specified."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "PSR Binding Assay",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "BVP Assay",
+      "assay_definition": "An ELISA-based assay that measures the binding of antibodies to immobilized baculovirus particles (BVP). A higher absorbance reading indicates greater nonspecific binding.",
+      "readout": {
+        "primary_metric_name": "BVP Score",
+        "raw_units": "Absorbance at 450 nm",
+        "normalized_units": "Fold-over-background",
+        "directionality": "lower_is_better",
+        "value_transformations": "BVP score was determined by normalizing the absorbance of the test antibody by the absorbance of control wells containing no test antibody."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "1 µM",
+        "buffer": "Blocking buffer: PBS with 0.5% BSA. Antibody dilution buffer is the same.",
+        "pH": "Coating buffer pH 9.6; blocking/assay buffer pH not specified, likely ~7.4 for PBS.",
+        "salt_or_additives": "Washes performed with PBS.",
+        "temperature": "Room temperature, except for overnight coating at 4 °C.",
+        "incubation_or_stress": "1 hour incubation with primary antibody."
+      },
+      "antigen_info": {
+        "antigen_used": "Baculovirus particles (BVP)",
+        "binding_state": "Immobilized on an ELISA plate overnight.",
+        "notes": "Source of BVP: BlueSky Biotech."
+      },
+      "platform_and_instrumentation": {
+        "platform": "ELISA",
+        "instrument_vendor_model": "Not specified, but plate absorbance reader.",
+        "columns_or_chips_or_surfaces": "Corning 3369 ELISA plates",
+        "detection_mode": "Absorbance at 450 nm after TMB substrate reaction."
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Reaction stopped with 2 M sulfuric acid. Absorbance read at 450 nm. Score calculated as fold-over-background.",
+        "controls_and_standards": "Control wells with no test antibody were used for background normalization.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 4.3 ± 2.2 Fold-over-background. Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "The instrument model for the plate reader is not specified.",
+        "The paper notes the analysis method (background being 'no antibody') differs from the original Hötzel et al. paper and may be 'over-stringent'."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "BVP Assay",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "2",
+          "location": "Further Details on the BVP Assay",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "HIC",
+      "assay_definition": "Hydrophobic Interaction Chromatography (HIC) measures the retention time of an antibody on a hydrophobic column under high salt conditions. It is a measure of surface hydrophobicity, which can correlate with nonspecific binding and poor developability. Longer retention time indicates greater hydrophobicity.",
+      "readout": {
+        "primary_metric_name": "Retention time",
+        "raw_units": "min",
+        "normalized_units": "",
+        "directionality": "lower_is_better",
+        "value_transformations": ""
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "5 µg (from 1 mg/mL stock)",
+        "buffer": "Mobile Phase A: 1.8 M ammonium sulfate and 0.1 M sodium phosphate. Mobile Phase B: 0.1 M sodium phosphate.",
+        "pH": "6.5",
+        "salt_or_additives": "Samples spiked with mobile phase A to a final ammonium sulfate concentration of ~1 M.",
+        "temperature": "Not specified",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "N/A (interaction is with a chemical surface)",
+        "binding_state": "N/A",
+        "notes": ""
+      },
+      "platform_and_instrumentation": {
+        "platform": "HPLC",
+        "instrument_vendor_model": "Not specified",
+        "columns_or_chips_or_surfaces": "Sepax Proteomix HIC butyl-NP5 column",
+        "detection_mode": "UV absorbance at 280 nm"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Analyzed with a linear gradient of mobile phase A to B over 20 min.",
+        "controls_and_standards": "Not specified.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 11.7 ± 0.6 min. Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "Although a measure of hydrophobicity, its inclusion as a 'polyreactivity' assay is interpretive, but it is a common developability assay that measures a related property.",
+        "The HPLC instrument vendor/model is not specified."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "HIC",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "replicates_and_statistics",
+    "qc_criteria",
+    "controls_and_standards",
+    "instrument_vendor_model (for ELISA and HIC)",
+    "temperature (for most assays)",
+    "n_replicates",
+    "error_bars",
+    "stat_tests"
+  ]
+}

assay_metadata/flab2/jain2017biophysical_HEK_assay_metadata.txt

@@ -0,0 +1,81 @@
+{
+  "endpoint": "expression",
+  "assay_variants": [
+    {
+      "assay_name_reported": "HEK titer",
+      "assay_definition": "Purified antibody yield from HEK293 cell culture supernatant.",
+      "readout": {
+        "primary_metric_name": "Titer / Purified Yield",
+        "raw_units": "HEK Titer (mg/L)",
+        "normalized_units": "HEK",
+        "directionality": "higher_is_better",
+        "value_transformations": ""
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "",
+        "buffer": "25 mM Hepes and 150 mM sodium chloride, pH 7.3 (final buffer after purification)",
+        "pH": "7.3 (final buffer after purification)",
+        "salt_or_additives": "150 mM sodium chloride (final buffer after purification)",
+        "temperature": "",
+        "incubation_or_stress": "6 days of growth"
+      },
+      "antigen_info": {
+        "antigen_used": "no antigen mentioned",
+        "binding_state": "",
+        "notes": "Antigen not used for quantification of expression."
+      },
+      "platform_and_instrumentation": {
+        "platform": "Protein A chromatography (for purification); Quantification method not specified",
+        "instrument_vendor_model": "MabSelect SuRe (GE Healthcare Life Sciences) for Protein A agarose",
+        "columns_or_chips_or_surfaces": "Protein A agarose",
+        "detection_mode": "Quantification method not specified"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Cell culture supernatant harvested by centrifugation, passed over Protein A agarose, washed with PBS, eluted, buffer-exchanged.",
+        "controls_and_standards": "",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": ""
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "The specific method for quantifying the purified antibody (e.g., A280, BCA) is not reported.",
+        "Transfection conditions (reagent, DNA amount/ratio, cell density) are not reported.",
+        "Culture conditions (media, temperature, CO2, shaking/bioreactor, scale/volume) are not reported beyond growth duration."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "6",
+          "location": "Table S2, Table S3",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "945",
+          "location": "Brief Description of Assays",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "949",
+          "location": "Materials and Methods -> Antibody Expression, Production, and Purification",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "Specific quantification method for purified protein (e.g., A280, BCA)",
+    "Transfection conditions (reagent, DNA amount/ratio, cell density)",
+    "Culture conditions (media, temperature, CO2, shaking/bioreactor, scale/volume)",
+    "Concentration of purified protein before buffer exchange",
+    "pH and salt/additives for culture media",
+    "Temperature for culture",
+    "N_replicates, error_bars, stat_tests"
+  ]
+}

assay_metadata/flab2/jain2017biophysical_PSR_assay_metadata.txt

@@ -0,0 +1,322 @@
+{
+  "endpoint": "polyreactivity",
+  "assay_variants": [
+    {
+      "assay_name_reported": "PSR Binding Assay",
+      "assay_definition": "A flow cytometry-based assay measuring the binding of yeast-displayed antibodies to a biotinylated polyspecificity reagent (PSR) derived from soluble CHO cell membrane proteins. Higher fluorescence indicates more nonspecific binding.",
+      "readout": {
+        "primary_metric_name": "Normalized Median Fluorescence Intensity (MFI)",
+        "raw_units": "Poly-Specficity Reagent (PSR) SMP Score (0-1)",
+        "normalized_units": "PSR",
+        "directionality": "lower_is_better",
+        "value_transformations": "MFI values were normalized from 0 to 1 based on three reference antibodies exhibiting low, medium, and high PSR MFI values."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG-presenting yeast",
+        "concentration": "Not specified",
+        "buffer": "Not specified",
+        "pH": "Not specified",
+        "salt_or_additives": "Secondary labeling mix included Extravidin-R-PE, anti-human LC-FITC, and propidium iodide.",
+        "temperature": "Not specified",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "Polyspecificity Reagent (PSR)",
+        "binding_state": "Soluble, biotinylated membrane proteins prepared from CHO cells.",
+        "notes": "The enriched membrane fraction was biotinylated using NHS-LC-Biotin."
+      },
+      "platform_and_instrumentation": {
+        "platform": "Flow Cytometry",
+        "instrument_vendor_model": "FACSCanto (BD Biosciences) using an HTS sample injector",
+        "columns_or_chips_or_surfaces": "",
+        "detection_mode": "Fluorescence (R-PE channel for nonspecific binding)."
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Flow cytometry data were analyzed for median fluorescence intensity (MFI) in the R-PE channel to assess nonspecific binding.",
+        "controls_and_standards": "Three reference antibodies exhibiting low, medium, and high PSR MFI values were used for normalization.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 0.27 ± 0.06 (no units provided for normalized score). Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "The exact composition and preparation of the yeast-displayed IgG is not detailed in the SI.",
+        "Buffer compositions for incubation and washing are not specified."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "PSR Binding Assay",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "CIC",
+      "assay_definition": "Cross-Interaction Chromatography (CIC) measures the retention time of an antibody on a column where polyclonal human antibodies are immobilized. A longer retention time indicates a higher degree of undesirable cross-interaction with other antibodies.",
+      "readout": {
+        "primary_metric_name": "Retention time",
+        "raw_units": "min",
+        "normalized_units": "",
+        "directionality": "lower_is_better",
+        "value_transformations": "The raw retention time is used directly."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "~5 µg tested",
+        "buffer": "PBS was used as the mobile phase.",
+        "pH": "Not specified, likely ~7.4 for PBS.",
+        "salt_or_additives": "",
+        "temperature": "Not specified",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "Human serum polyclonal antibodies",
+        "binding_state": "Immobilized on a HiTrap column.",
+        "notes": "The polyclonal antibodies represent a diverse set of potential interaction partners."
+      },
+      "platform_and_instrumentation": {
+        "platform": "HPLC",
+        "instrument_vendor_model": "Agilent 1100 series HPLC system",
+        "columns_or_chips_or_surfaces": "1-mL HiTrap column (17-0716-01; GE Healthcare) coupled with ~30 mg of polyclonal antibodies (I4506; Sigma).",
+        "detection_mode": "Not specified, but typical for HPLC is UV absorbance."
+      },
+      "analysis_pipeline": {
+        "processing_steps": "The retention time of the major peak was assigned as the result.",
+        "controls_and_standards": "Not specified.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 10.1 ± 0.5 min. Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "The pH of the PBS mobile phase is not explicitly stated.",
+        "The detection method (e.g., UV wavelength) is not specified.",
+        "Details on controls and standards are not provided."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "CIC",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "BVP Assay",
+      "assay_definition": "An ELISA-based assay that measures the binding of antibodies to immobilized baculovirus particles (BVP). A higher absorbance reading indicates greater nonspecific binding.",
+      "readout": {
+        "primary_metric_name": "BVP Score",
+        "raw_units": "Absorbance at 450 nm",
+        "normalized_units": "Fold-over-background",
+        "directionality": "lower_is_better",
+        "value_transformations": "BVP score was determined by normalizing the absorbance of the test antibody by the absorbance of control wells containing no test antibody."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "1 µM",
+        "buffer": "Blocking buffer: PBS with 0.5% BSA. Antibody dilution buffer is the same.",
+        "pH": "Coating buffer pH 9.6; blocking/assay buffer pH not specified, likely ~7.4 for PBS.",
+        "salt_or_additives": "Washes performed with PBS.",
+        "temperature": "Room temperature, except for overnight coating at 4 °C.",
+        "incubation_or_stress": "1 hour incubation with primary antibody."
+      },
+      "antigen_info": {
+        "antigen_used": "Baculovirus particles (BVP)",
+        "binding_state": "Immobilized on an ELISA plate overnight.",
+        "notes": "Source of BVP: BlueSky Biotech."
+      },
+      "platform_and_instrumentation": {
+        "platform": "ELISA",
+        "instrument_vendor_model": "Not specified, but plate absorbance reader.",
+        "columns_or_chips_or_surfaces": "Corning 3369 ELISA plates",
+        "detection_mode": "Absorbance at 450 nm after TMB substrate reaction."
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Reaction stopped with 2 M sulfuric acid. Absorbance read at 450 nm. Score calculated as fold-over-background.",
+        "controls_and_standards": "Control wells with no test antibody were used for background normalization.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 4.3 ± 2.2 Fold-over-background. Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "The instrument model for the plate reader is not specified.",
+        "The paper notes the analysis method (background being 'no antibody') differs from the original Hötzel et al. paper and may be 'over-stringent'."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "BVP Assay",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "2",
+          "location": "Further Details on the BVP Assay",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "ELISA",
+      "assay_definition": "A multi-antigen ELISA measuring antibody binding to a panel of six different nonspecific antigens: cardiolipin, KLH, LPS, ssDNA, dsDNA, and insulin.",
+      "readout": {
+        "primary_metric_name": "ELISA Score",
+        "raw_units": "Absorbance at 450 nm",
+        "normalized_units": "Fold-over-background",
+        "directionality": "lower_is_better",
+        "value_transformations": "The final reported value is a single 'Fold-over-background' score, implying a composite or averaged result from the six antigens."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "100 nM",
+        "buffer": "Blocking buffer: PBS with 0.5% BSA.",
+        "pH": "Not specified, likely ~7.4 for PBS.",
+        "salt_or_additives": "Washes performed with PBST (PBS plus 0.1% Tween 20).",
+        "temperature": "Room temperature, except for overnight coating at 4 °C.",
+        "incubation_or_stress": "1 hour incubation with antibody."
+      },
+      "antigen_info": {
+        "antigen_used": "Cardiolipin, Keyhole limpet hemocyanin (KLH), Lipopolysaccharide (LPS), single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), insulin.",
+        "binding_state": "Immobilized individually on ELISA plates.",
+        "notes": "All antigens sourced from Sigma or InvivoGen, catalog numbers provided."
+      },
+      "platform_and_instrumentation": {
+        "platform": "ELISA",
+        "instrument_vendor_model": "Not specified",
+        "columns_or_chips_or_surfaces": "Corning 3369 ELISA plates",
+        "detection_mode": "Absorbance at 450 nm"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Procedure follows the BVP assay after the coating step. The method for combining the readouts from the six antigens into a single score is not detailed.",
+        "controls_and_standards": "Not specified, but likely uses a 'no antibody' background control similar to the BVP assay.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 1.9 ± 1.0 Fold-over-background. Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "The method for calculating the single 'ELISA' score from the six different antigen wells is not described.",
+        "The instrument model for the plate reader is not specified."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "ELISA",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "HIC",
+      "assay_definition": "Hydrophobic Interaction Chromatography (HIC) measures the retention time of an antibody on a hydrophobic column under high salt conditions. It is a measure of surface hydrophobicity, which can correlate with nonspecific binding and poor developability. Longer retention time indicates greater hydrophobicity.",
+      "readout": {
+        "primary_metric_name": "Retention time",
+        "raw_units": "min",
+        "normalized_units": "",
+        "directionality": "lower_is_better",
+        "value_transformations": ""
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "5 µg (from 1 mg/mL stock)",
+        "buffer": "Mobile Phase A: 1.8 M ammonium sulfate and 0.1 M sodium phosphate. Mobile Phase B: 0.1 M sodium phosphate.",
+        "pH": "6.5",
+        "salt_or_additives": "Samples spiked with mobile phase A to a final ammonium sulfate concentration of ~1 M.",
+        "temperature": "Not specified",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "N/A (interaction is with a chemical surface)",
+        "binding_state": "N/A",
+        "notes": ""
+      },
+      "platform_and_instrumentation": {
+        "platform": "HPLC",
+        "instrument_vendor_model": "Not specified",
+        "columns_or_chips_or_surfaces": "Sepax Proteomix HIC butyl-NP5 column",
+        "detection_mode": "UV absorbance at 280 nm"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Analyzed with a linear gradient of mobile phase A to B over 20 min.",
+        "controls_and_standards": "Not specified.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 11.7 ± 0.6 min. Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "Although a measure of hydrophobicity, its inclusion as a 'polyreactivity' assay is interpretive, but it is a common developability assay that measures a related property.",
+        "The HPLC instrument vendor/model is not specified."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "HIC",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "replicates_and_statistics",
+    "qc_criteria",
+    "controls_and_standards",
+    "instrument_vendor_model (for ELISA and HIC)",
+    "temperature (for most assays)",
+    "n_replicates",
+    "error_bars",
+    "stat_tests"
+  ]
+}

assay_metadata/flab2/jain2017biophysical_SAS_assay_metadata.txt

@@ -0,0 +1,75 @@
+{
+  "endpoint": "self-aggregation",
+  "assay_variants": [
+    {
+      "assay_name_reported": "Accelerated Stability by SEC (AS SEC Slope)",
+      "assay_definition": "Measures the rate of aggregation by quantifying the loss of monomer over time during thermal stress. A linear slope of monomer loss versus time is calculated from measurements at multiple timepoints.",
+      "readout": {
+        "primary_metric_name": "Monomer percentage loss per day",
+        "raw_units": "Slope for Accelerated Stability",
+        "normalized_units": "SAS",
+        "directionality": "lower_is_better",
+        "value_transformations": "A linear slope is calculated from the percentage of aggregated species at different time points (days 0, 5, 20, and 30)."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "1 mg/mL",
+        "buffer": "HBS (25 mM Hepes and 150 mM sodium chloride, pH 7.3)",
+        "pH": "7.3",
+        "salt_or_additives": "150 mM sodium chloride",
+        "temperature": "40 °C",
+        "incubation_or_stress": "Samples were incubated at 40°C for 30 days, with time points taken at day 0, 5, 20, and 30."
+      },
+      "antigen_info": {
+        "antigen_used": "false",
+        "binding_state": "unbound",
+        "notes": "no antigen mentioned"
+      },
+      "platform_and_instrumentation": {
+        "platform": "Size-Exclusion Chromatography (SEC)",
+        "instrument_vendor_model": "Inferred to be Agilent 1100 series HPLC system",
+        "columns_or_chips_or_surfaces": "SEC Column (0022855; Tosoh Bioscience)",
+        "detection_mode": "Not specified, likely UV absorbance."
+      },
+      "analysis_pipeline": {
+        "processing_steps": "A long-term stability slope was calculated from the percent aggregated, measured on the SEC at time points 0, 5, 20, and 30 days.",
+        "controls_and_standards": "The measurement at day 0 serves as the baseline control for each sample.",
+        "qc_criteria": "Not specified",
+        "reported_thresholds_or_bins": "The 'Worst 10% threshold' for approved antibodies was determined to be 0.08 +/- 0.03 % monomer loss per day."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "The error for the threshold (±0.03) is reported as a standard deviation based on bootstrapping.",
+        "stat_tests": "Anderson-Darling test was used to compare the AS distributions between clinical phases (p=0.03)."
+      },
+      "notes_on_ambiguity": [
+        "The detection method for the SEC analysis is not explicitly stated but is typically UV absorbance.",
+        "The HPLC system model is inferred from descriptions of other chromatography-based assays in the paper."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "AS SEC Slope",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "2",
+          "location": "Brief Description of Assays",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "AS-SEC: detection mode",
+    "AS-SEC: instrument_vendor_model (inferred)"
+  ]
+}

assay_metadata/flab2/jain2017biophysical_SGACSINS_assay_metadata.txt

@@ -0,0 +1,75 @@
+{
+  "endpoint": "self-aggregation",
+  "assay_variants": [
+    {
+      "assay_name_reported": "SGAC-SINS (salt-gradient affinity-capture self-interaction nanoparticle spectroscopy)",
+      "assay_definition": "Measures the propensity of an antibody to self-associate under salt stress. The metric (SGAC100) is the extrapolated concentration of ammonium sulfate (mM) required to induce a specific, fixed wavelength shift (560 nm) of antibody-coated gold nanoparticles, indicating a defined level of aggregation.",
+      "readout": {
+        "primary_metric_name": "SGAC100 (Ammonium Sulfate Concentration for 560nm shift)",
+        "raw_units": "SGAC-SINS AS100 ((NH4)2SO4 mM)",
+        "normalized_units": "SGACSINS",
+        "directionality": "higher_is_better",
+        "value_transformations": "The ammonium sulfate concentration that induces a 560nm wavelength shift is determined by extrapolation from a curve of wavelength shifts vs. salt concentration."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "Not specified",
+        "buffer": "Antibodies are in a base buffer (assumed 25 mM Hepes, 150 mM NaCl, pH 7.3) before being diluted into the salt gradient.",
+        "pH": "7.3",
+        "salt_or_additives": "Ammonium sulfate, titrated in steps from 300 mM to 1,000 mM.",
+        "temperature": "Not specified (Assumed room temperature)",
+        "incubation_or_stress": "Incubated with nanoparticles for 30 min, then for an additional 1.5 hours after addition of ammonium sulfate."
+      },
+      "antigen_info": {
+        "antigen_used": "false",
+        "binding_state": "unbound",
+        "notes": "no antigen mentioned"
+      },
+      "platform_and_instrumentation": {
+        "platform": "Nanoparticle Spectroscopy",
+        "instrument_vendor_model": "Molecular Devices SpectraMax M2 with SoftMax Pro6 software",
+        "columns_or_chips_or_surfaces": "Gold nanoparticles (Ted Pella Inc.) coated with anti-human IgG Fc (Jackson ImmunoResearch) and a non-specific polyclonal antibody.",
+        "detection_mode": "Plasmon wavelength absorbance"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "A graph of wavelength shift vs. ammonium sulfate concentration is generated. The concentration at which the shift would be 560 nm is extrapolated. If the shift never reaches 560 nm, a value of 1,000 mM is assigned.",
+        "controls_and_standards": "Not specified, but the analysis is relative to a fixed wavelength shift, which serves as an internal standard.",
+        "qc_criteria": "Not specified",
+        "reported_thresholds_or_bins": "The 'Worst 10% threshold' for approved antibodies was determined to be 370 +/- 133 mM. Values below this (i.e., requiring less salt to aggregate) are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "The error for the threshold (±133 mM) is reported as a standard deviation based on bootstrapping.",
+        "stat_tests": "Not specified for this specific assay, but general statistical methods are described."
+      },
+      "notes_on_ambiguity": [
+        "The exact antibody concentration used in the assay is not specified.",
+        "The temperature for the incubations is not specified."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "SGAC-SINS",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "2",
+          "location": "Brief Description of Assays",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "SGAC-SINS: antibody concentration",
+    "SGAC-SINS: assay temperature"
+  ]
+}

assay_metadata/flab2/jain2017biophysical_SMACRT_assay_metadata.txt

@@ -0,0 +1,382 @@
+{
+  "endpoint": "polyreactivity",
+  "assay_variants": [
+    {
+      "assay_name_reported": "SMAC",
+      "assay_definition": "Standup Monolayer Adsorption Chromatography (SMAC) is used to assess antibody properties by measuring retention time on a size-exclusion column under specific salt conditions. In this context, it is grouped with assays that measure self-association or interaction with a column matrix under salt-stress. A longer retention time is considered unfavorable.",
+      "readout": {
+        "primary_metric_name": "Retention time",
+        "raw_units": "SMAC Retention Time (Min)a",
+        "normalized_units": "SMAC",
+        "directionality": "lower_is_better",
+        "value_transformations": "The retention time of the major peak is used as the result."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "2 µg injected",
+        "buffer": "Running buffer: 150 mM sodium phosphate",
+        "pH": "7.0",
+        "salt_or_additives": "150 mM sodium phosphate",
+        "temperature": "Not specified",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "N/A (interaction is with a chemical surface)",
+        "binding_state": "N/A",
+        "notes": "The interaction is with the column matrix itself, not a biological antigen."
+      },
+      "platform_and_instrumentation": {
+        "platform": "Chromatography",
+        "instrument_vendor_model": "Not specified",
+        "columns_or_chips_or_surfaces": "Zenix SEC-300 column (213300-4630; Sepax Technologies)",
+        "detection_mode": "Not specified, likely UV absorbance."
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Retention time for each sample was assigned based on the major peak.",
+        "controls_and_standards": "Not specified.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 12.8 ± 1.2 min. Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "While requested under 'polyreactivity', the paper groups SMAC with assays measuring self-interaction and interaction with column matrices under salt-stress, not classical polyreactivity with diverse biological reagents.",
+        "The HPLC instrument vendor/model is not specified."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "SMAC",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "CIC",
+      "assay_definition": "Cross-Interaction Chromatography (CIC) measures the retention time of an antibody on a column where polyclonal human antibodies are immobilized. A longer retention time indicates a higher degree of undesirable cross-interaction with other antibodies.",
+      "readout": {
+        "primary_metric_name": "Retention time",
+        "raw_units": "min",
+        "normalized_units": "",
+        "directionality": "lower_is_better",
+        "value_transformations": "The raw retention time is used directly."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "~5 µg tested",
+        "buffer": "PBS was used as the mobile phase.",
+        "pH": "Not specified, likely ~7.4 for PBS.",
+        "salt_or_additives": "",
+        "temperature": "Not specified",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "Human serum polyclonal antibodies",
+        "binding_state": "Immobilized on a HiTrap column.",
+        "notes": "The polyclonal antibodies represent a diverse set of potential interaction partners."
+      },
+      "platform_and_instrumentation": {
+        "platform": "HPLC",
+        "instrument_vendor_model": "Agilent 1100 series HPLC system",
+        "columns_or_chips_or_surfaces": "1-mL HiTrap column (17-0716-01; GE Healthcare) coupled with ~30 mg of polyclonal antibodies (I4506; Sigma).",
+        "detection_mode": "Not specified, but typical for HPLC is UV absorbance."
+      },
+      "analysis_pipeline": {
+        "processing_steps": "The retention time of the major peak was assigned as the result.",
+        "controls_and_standards": "Not specified.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 10.1 ± 0.5 min. Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "The pH of the PBS mobile phase is not explicitly stated.",
+        "The detection method (e.g., UV wavelength) is not specified.",
+        "Details on controls and standards are not provided."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "CIC",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "PSR Binding Assay",
+      "assay_definition": "A flow cytometry-based assay measuring the binding of yeast-displayed antibodies to a biotinylated polyspecificity reagent (PSR) derived from soluble CHO cell membrane proteins. Higher fluorescence indicates more nonspecific binding.",
+      "readout": {
+        "primary_metric_name": "Normalized Median Fluorescence Intensity (MFI)",
+        "raw_units": "MFI in R-PE channel",
+        "normalized_units": "Normalized score (0 to 1)",
+        "directionality": "lower_is_better",
+        "value_transformations": "MFI values were normalized from 0 to 1 based on three reference antibodies exhibiting low, medium, and high PSR MFI values."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG-presenting yeast",
+        "concentration": "Not specified",
+        "buffer": "Not specified",
+        "pH": "Not specified",
+        "salt_or_additives": "Secondary labeling mix included Extravidin-R-PE, anti-human LC-FITC, and propidium iodide.",
+        "temperature": "Not specified",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "Polyspecificity Reagent (PSR)",
+        "binding_state": "Soluble, biotinylated membrane proteins prepared from CHO cells.",
+        "notes": "The enriched membrane fraction was biotinylated using NHS-LC-Biotin."
+      },
+      "platform_and_instrumentation": {
+        "platform": "Flow Cytometry",
+        "instrument_vendor_model": "FACSCanto (BD Biosciences) using an HTS sample injector",
+        "columns_or_chips_or_surfaces": "",
+        "detection_mode": "Fluorescence (R-PE channel for nonspecific binding)."
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Flow cytometry data were analyzed for median fluorescence intensity (MFI) in the R-PE channel to assess nonspecific binding.",
+        "controls_and_standards": "Three reference antibodies exhibiting low, medium, and high PSR MFI values were used for normalization.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 0.27 ± 0.06 (no units provided for normalized score). Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "The exact composition and preparation of the yeast-displayed IgG is not detailed in the SI.",
+        "Buffer compositions for incubation and washing are not specified."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "PSR Binding Assay",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "BVP Assay",
+      "assay_definition": "An ELISA-based assay that measures the binding of antibodies to immobilized baculovirus particles (BVP). A higher absorbance reading indicates greater nonspecific binding.",
+      "readout": {
+        "primary_metric_name": "BVP Score",
+        "raw_units": "Absorbance at 450 nm",
+        "normalized_units": "Fold-over-background",
+        "directionality": "lower_is_better",
+        "value_transformations": "BVP score was determined by normalizing the absorbance of the test antibody by the absorbance of control wells containing no test antibody."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "1 µM",
+        "buffer": "Blocking buffer: PBS with 0.5% BSA. Antibody dilution buffer is the same.",
+        "pH": "Coating buffer pH 9.6; blocking/assay buffer pH not specified, likely ~7.4 for PBS.",
+        "salt_or_additives": "Washes performed with PBS.",
+        "temperature": "Room temperature, except for overnight coating at 4 °C.",
+        "incubation_or_stress": "1 hour incubation with primary antibody."
+      },
+      "antigen_info": {
+        "antigen_used": "Baculovirus particles (BVP)",
+        "binding_state": "Immobilized on an ELISA plate overnight.",
+        "notes": "Source of BVP: BlueSky Biotech."
+      },
+      "platform_and_instrumentation": {
+        "platform": "ELISA",
+        "instrument_vendor_model": "Not specified, but plate absorbance reader.",
+        "columns_or_chips_or_surfaces": "Corning 3369 ELISA plates",
+        "detection_mode": "Absorbance at 450 nm after TMB substrate reaction."
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Reaction stopped with 2 M sulfuric acid. Absorbance read at 450 nm. Score calculated as fold-over-background.",
+        "controls_and_standards": "Control wells with no test antibody were used for background normalization.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 4.3 ± 2.2 Fold-over-background. Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "The instrument model for the plate reader is not specified.",
+        "The paper notes the analysis method (background being 'no antibody') differs from the original Hötzel et al. paper and may be 'over-stringent'."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "BVP Assay",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "2",
+          "location": "Further Details on the BVP Assay",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "ELISA",
+      "assay_definition": "A multi-antigen ELISA measuring antibody binding to a panel of six different nonspecific antigens: cardiolipin, KLH, LPS, ssDNA, dsDNA, and insulin.",
+      "readout": {
+        "primary_metric_name": "ELISA Score",
+        "raw_units": "Absorbance at 450 nm",
+        "normalized_units": "Fold-over-background",
+        "directionality": "lower_is_better",
+        "value_transformations": "The final reported value is a single 'Fold-over-background' score, implying a composite or averaged result from the six antigens."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "100 nM",
+        "buffer": "Blocking buffer: PBS with 0.5% BSA.",
+        "pH": "Not specified, likely ~7.4 for PBS.",
+        "salt_or_additives": "Washes performed with PBST (PBS plus 0.1% Tween 20).",
+        "temperature": "Room temperature, except for overnight coating at 4 °C.",
+        "incubation_or_stress": "1 hour incubation with antibody."
+      },
+      "antigen_info": {
+        "antigen_used": "Cardiolipin, Keyhole limpet hemocyanin (KLH), Lipopolysaccharide (LPS), single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), insulin.",
+        "binding_state": "Immobilized individually on ELISA plates.",
+        "notes": "All antigens sourced from Sigma or InvivoGen, catalog numbers provided."
+      },
+      "platform_and_instrumentation": {
+        "platform": "ELISA",
+        "instrument_vendor_model": "Not specified",
+        "columns_or_chips_or_surfaces": "Corning 3369 ELISA plates",
+        "detection_mode": "Absorbance at 450 nm"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Procedure follows the BVP assay after the coating step. The method for combining the readouts from the six antigens into a single score is not detailed.",
+        "controls_and_standards": "Not specified, but likely uses a 'no antibody' background control similar to the BVP assay.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 1.9 ± 1.0 Fold-over-background. Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "The method for calculating the single 'ELISA' score from the six different antigen wells is not described.",
+        "The instrument model for the plate reader is not specified."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "ELISA",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    },
+    {
+      "assay_name_reported": "HIC",
+      "assay_definition": "Hydrophobic Interaction Chromatography (HIC) measures the retention time of an antibody on a hydrophobic column under high salt conditions. It is a measure of surface hydrophobicity, which can correlate with nonspecific binding and poor developability. Longer retention time indicates greater hydrophobicity.",
+      "readout": {
+        "primary_metric_name": "Retention time",
+        "raw_units": "min",
+        "normalized_units": "",
+        "directionality": "lower_is_better",
+        "value_transformations": ""
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "5 µg (from 1 mg/mL stock)",
+        "buffer": "Mobile Phase A: 1.8 M ammonium sulfate and 0.1 M sodium phosphate. Mobile Phase B: 0.1 M sodium phosphate.",
+        "pH": "6.5",
+        "salt_or_additives": "Samples spiked with mobile phase A to a final ammonium sulfate concentration of ~1 M.",
+        "temperature": "Not specified",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "N/A (interaction is with a chemical surface)",
+        "binding_state": "N/A",
+        "notes": ""
+      },
+      "platform_and_instrumentation": {
+        "platform": "HPLC",
+        "instrument_vendor_model": "Not specified",
+        "columns_or_chips_or_surfaces": "Sepax Proteomix HIC butyl-NP5 column",
+        "detection_mode": "UV absorbance at 280 nm"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Analyzed with a linear gradient of mobile phase A to B over 20 min.",
+        "controls_and_standards": "Not specified.",
+        "qc_criteria": "Not specified.",
+        "reported_thresholds_or_bins": "Worst 10% threshold for approved antibodies: 11.7 ± 0.6 min. Values above this are considered a 'red flag'."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "Although a measure of hydrophobicity, its inclusion as a 'polyreactivity' assay is interpretive, but it is a common developability assay that measures a related property.",
+        "The HPLC instrument vendor/model is not specified."
+      ],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "1",
+          "location": "HIC",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "replicates_and_statistics",
+    "qc_criteria",
+    "controls_and_standards",
+    "instrument_vendor_model (for ELISA, HIC, SMAC)",
+    "temperature (for most assays)",
+    "n_replicates",
+    "error_bars",
+    "stat_tests"
+  ]
+}

assay_metadata/flab2/jain2017biophysical_Tm_assay_metadata.txt

@@ -0,0 +1,88 @@
+{
+  "endpoint": "thermostability",
+  "assay_variants": [
+    {
+      "assay_name_reported": "Fab Tm by DSF",
+      "assay_definition": "The melting temperature (Tm) of the Fab domain of clinical-stage therapeutic antibodies, determined by differential scanning fluorimetry (DSF). The Tm represents the midpoint of the protein's thermal unfolding transition.",
+      "readout": {
+        "primary_metric_name": "Tm",
+        "raw_units": "Fab Tm by DSF (degreeC)",
+        "normalized_units": "DSF",
+        "directionality": "higher_is_better",
+        "value_transformations": "The melting temperature (Tm) was defined as the temperature at the minimum of the negative first derivative of the fluorescence intensity versus temperature."
+      },
+      "sample_and_format": {
+        "molecule_format": "Fab",
+        "concentration": "0.1 mg/mL",
+        "buffer": "PBS",
+        "pH": "7.4",
+        "salt_or_additives": "",
+        "temperature": "20-95 °C",
+        "incubation_or_stress": "Antibodies were enzymatically digested to generate Fab fragments prior to the assay."
+      },
+      "antigen_info": {
+        "antigen_used": "false",
+        "binding_state": "unbound",
+        "notes": "no antigen mentioned"
+      },
+      "platform_and_instrumentation": {
+        "platform": "DSF (Differential Scanning Fluorimetry)",
+        "instrument_vendor_model": "Thermofluor instrument (Johnson & Johnson)",
+        "columns_or_chips_or_surfaces": "96-well PCR plates",
+        "detection_mode": "Fluorescence intensity using SYPRO Orange dye"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "The melting temperature (Tm) was defined as the temperature at the minimum of the negative first derivative of the fluorescence intensity vs. temperature data. Data were analyzed using proprietary software.",
+        "controls_and_standards": "",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": "The paper reports a range of Tm values from 64 °C to 93 °C for the clinical-stage antibodies."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "2",
+        "error_bars": "The reported Tm is the average of two separate measurements.",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [],
+      "evidence": [
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "8",
+          "location": "Supporting Information, Materials and Methods, Differential Scanning Fluorimetry (DSF)",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "8",
+          "location": "Supporting Information, Materials and Methods, Differential Scanning Fluorimetry (DSF)",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "8",
+          "location": "Supporting Information, Materials and Methods, Differential Scanning Fluorimetry (DSF)",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "pnas.201616408si.pdf",
+          "page": "8",
+          "location": "Supporting Information, Materials and Methods, Antibody Digestion.",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "jain-et-al-2017-biophysical-properties-of-the-clinical-stage-antibody-landscape.pdf",
+          "page": "3",
+          "location": "Results and Discussion",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "salt_or_additives",
+    "columns_or_chips_or_surfaces",
+    "controls_and_standards",
+    "qc_criteria",
+    "error_bars",
+    "stat_tests"
+  ]
+}

assay_metadata/flab2/jain2023identifying_DNP_assay_metadata.txt

@@ -0,0 +1,74 @@
+{
+  "endpoint": "polyreactivity",
+  "assay_variants": [
+    {
+      "assay_name_reported": "DNP Binding Assay",
+      "assay_definition": "An assay measuring binding to 2,4-dinitrophenol (DNP). It is clustered with BVP and multi-antigen ELISA, suggesting it serves as a proxy for polyreactivity. Higher binding is considered unfavorable.",
+      "readout": {
+        "primary_metric_name": "DNP Binding Score",
+        "raw_units": "DNP",
+        "normalized_units": "DNP",
+        "directionality": "lower_is_better",
+        "value_transformations": "The specific units or value transformation (e.g., fold-change, OD) are not specified in the main paper; they are likely in the supplementary information."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1 (inferred from context of other assays in the paper)",
+        "concentration": "",
+        "buffer": "",
+        "pH": "",
+        "salt_or_additives": "",
+        "temperature": "",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "2,4-dinitrophenol (DNP)",
+        "binding_state": "",
+        "notes": ""
+      },
+      "platform_and_instrumentation": {
+        "platform": "",
+        "instrument_vendor_model": "",
+        "columns_or_chips_or_surfaces": "",
+        "detection_mode": ""
+      },
+      "analysis_pipeline": {
+        "processing_steps": "",
+        "controls_and_standards": "",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": "The 90% threshold for the 64 approved mAbs in 2022 is 1.24 ± 0.57."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "The detailed experimental protocol for the DNP assay is not in the main PDF and is expected to be in the supplementary files, which could not be read.",
+        "Specifics of the readout (e.g., OD, fluorescence), antibody format, concentration, buffer, platform, and analysis pipeline are missing."
+      ],
+      "evidence": [
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "3",
+          "location": "Table 2",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "5",
+          "location": "Table 3",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "assay_definition (details)",
+    "readout (value_transformations)",
+    "sample_and_format (all fields)",
+    "antigen_info (binding_state)",
+    "platform_and_instrumentation (all fields)",
+    "analysis_pipeline (most fields)",
+    "replicates_and_statistics (all fields)"
+  ]
+}

assay_metadata/flab2/jain2023identifying_FA2_assay_metadata.txt

@@ -0,0 +1,80 @@
+{
+  "endpoint": "polyreactivity",
+  "assay_variants": [
+    {
+      "assay_name_reported": "Folate Binding Assay (FA)",
+      "assay_definition": "An assay measuring polyreactivity to the cofactor Folate (FA). It is clustered with Heme binding and Heparin Retention Time, and considered a proxy for polyreactivity or pinocytosis. Higher binding is considered unfavorable.",
+      "readout": {
+        "primary_metric_name": "Folate Binding Score",
+        "raw_units": "FA.2",
+        "normalized_units": "FA",
+        "directionality": "lower_is_better",
+        "value_transformations": "The specific units or value transformation (e.g., fold-change, OD) are not specified in the main paper; they are likely in the supplementary information."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1 (inferred from context of other assays in the paper)",
+        "concentration": "",
+        "buffer": "",
+        "pH": "",
+        "salt_or_additives": "",
+        "temperature": "",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "Folate (FA)",
+        "binding_state": "",
+        "notes": "This assay measures binding to the cofactor folate."
+      },
+      "platform_and_instrumentation": {
+        "platform": "",
+        "instrument_vendor_model": "",
+        "columns_or_chips_or_surfaces": "",
+        "detection_mode": ""
+      },
+      "analysis_pipeline": {
+        "processing_steps": "",
+        "controls_and_standards": "",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": "The 90% threshold for the 48 approved mAbs in 2022 is 3.52 ± 1.46."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "The detailed experimental protocol for the Folate (FA) assay is not in the main PDF and is expected to be in the supplementary files, which could not be read.",
+        "Specifics of the readout (e.g., raw units, value transformation), antibody format, concentration, buffer, platform, and analysis pipeline are missing."
+      ],
+      "evidence": [
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "3",
+          "location": "Table 2",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "5",
+          "location": "Table 3",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "3",
+          "location": "Text body",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "assay_definition (details)",
+    "readout (value_transformations and raw units)",
+    "sample_and_format (all fields)",
+    "antigen_info (binding_state)",
+    "platform_and_instrumentation (all fields)",
+    "analysis_pipeline (most fields)",
+    "replicates_and_statistics (all fields)"
+  ]
+}

assay_metadata/flab2/jain2023identifying_FVC32_assay_metadata.txt

@@ -0,0 +1,80 @@
+{
+  "endpoint": "polyreactivity",
+  "assay_variants": [
+    {
+      "assay_name_reported": "Fe2+ Induced Polyreactivity to C3 (Fe.C3.2)",
+      "assay_definition": "An assay measuring 'induced polyreactivity'. This is the binding of an antibody to Complement C3 protein after the antibody has been exposed to Fe2+ (iron). This indicates a change in binding profile upon oxidative stress. Higher binding is considered unfavorable.",
+      "readout": {
+        "primary_metric_name": "Induced C3 Binding Score",
+        "raw_units": "Fe.C3.2",
+        "normalized_units": "FeC3",
+        "directionality": "lower_is_better",
+        "value_transformations": "The specific units or value transformation (e.g., fold-change, OD) are not specified in the main paper; they are likely in the original source publication."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1 (inferred from context of other assays in the paper)",
+        "concentration": "",
+        "buffer": "",
+        "pH": "",
+        "salt_or_additives": "Antibodies are exposed to Fe2+ to induce the polyreactive state.",
+        "temperature": "",
+        "incubation_or_stress": "Exposure to Fe2+."
+      },
+      "antigen_info": {
+        "antigen_used": "Complement C3 protein",
+        "binding_state": "",
+        "notes": "This assay measures binding to C3 after inducement by an external stressor (Fe2+)."
+      },
+      "platform_and_instrumentation": {
+        "platform": "",
+        "instrument_vendor_model": "",
+        "columns_or_chips_or_surfaces": "",
+        "detection_mode": ""
+      },
+      "analysis_pipeline": {
+        "processing_steps": "",
+        "controls_and_standards": "",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": "The 90% threshold for the 50 approved mAbs in 2022 is 4.69 ± 0.62."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "This paper is a review article. The detailed experimental protocol for the induced polyreactivity assay is not included and is expected to be in the original source publication (likely reference 6, Lecerf et al., 2022).",
+        "Specifics of the readout (e.g., raw units, value transformation), antibody format, concentration, buffer, platform, and analysis pipeline are missing."
+      ],
+      "evidence": [
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "3",
+          "location": "Table 2",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "5",
+          "location": "Table 3",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "3",
+          "location": "Text body",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "assay_definition (details)",
+    "readout (value_transformations and raw units)",
+    "sample_and_format (most fields)",
+    "antigen_info (binding_state)",
+    "platform_and_instrumentation (all fields)",
+    "analysis_pipeline (most fields)",
+    "replicates_and_statistics (all fields)"
+  ]
+}

assay_metadata/flab2/jain2023identifying_FcRnRelRT3_assay_metadata.txt

@@ -0,0 +1,91 @@
+{
+  "endpoint": "pharmacokinetics",
+  "assay_variants": [
+    {
+      "assay_name_reported": "FcRn Column Retention Time",
+      "assay_definition": "This is an in vitro affinity chromatography assay that measures the retention time (RT) of an antibody on a column functionalized with the neonatal Fc receptor (FcRn) at acidic pH (6.0). This assay serves as an in vitro surrogate for in vivo pharmacokinetics, where longer retention time is expected to correlate with slower clearance and longer half-life. The final reported metric is the retention time relative to a control mAb.",
+      "readout": {
+        "primary_metric_name": "Relative Retention Time (FcRn Rel RT)",
+        "raw_units": "FcRn.Rel.RT.3",
+        "normalized_units": "FcRnRT",
+        "directionality": "higher_is_better",
+        "value_transformations": "The measured retention time is normalized by the retention time of a control mAb."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "Not specified",
+        "buffer": "Running buffer at pH 6.0 to facilitate binding to FcRn.",
+        "pH": "6.0",
+        "salt_or_additives": "Not specified",
+        "temperature": "Not specified",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "no antigen/target context mentioned",
+        "binding_state": "",
+        "notes": "This assay measures binding to FcRn, not the therapeutic target of the antibodies."
+      },
+      "platform_and_instrumentation": {
+        "platform": "Affinity Chromatography (likely HPLC)",
+        "instrument_vendor_model": "Not specified",
+        "columns_or_chips_or_surfaces": "FcRn column",
+        "detection_mode": "Not specified (likely UV absorbance)"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "The retention time of each antibody on the FcRn column is measured and then normalized to the retention time of a control mAb to yield the 'FcRn Rel RT'.",
+        "controls_and_standards": "A control mAb is used for normalization.",
+        "qc_criteria": "Not specified",
+        "reported_thresholds_or_bins": "A cutoff of 1.6 min for FcRn retention time (RT) was suggested based on correlation with in vivo clearance data from another study (Avery et al., 2018)."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "The paper does not report direct in vivo pharmacokinetics data (e.g., clearance, half-life). It reports results from an in vitro FcRn binding assay which is a surrogate for PK.",
+        "The specific identity of the control mAb used for normalization is not disclosed.",
+        "The '.3' suffix in 'FcRn.Rel.RT.3' likely refers to the data's literature source as mapped in the paper's correlation matrix (Figure 1), not a direct parameter of the assay itself."
+      ],
+      "evidence": [
+        {
+          "source_file": "kmab_a_2200540_sm7528.docx",
+          "page": "",
+          "location": "Definitions",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "kmab_a_2200540_sm7528.docx",
+          "page": "",
+          "location": "Definitions",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "3",
+          "location": "Table 2",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "16",
+          "location": "Figure 10D",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "3",
+          "location": "Results, In vitro measurements",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "instrument_vendor_model",
+    "column details (vendor, type)",
+    "detection_mode",
+    "control mAb identity",
+    "n_replicates"
+  ]
+}

assay_metadata/flab2/jain2023identifying_FvFVIII2_assay_metadata.txt

@@ -0,0 +1,80 @@
+{
+  "endpoint": "polyreactivity",
+  "assay_variants": [
+    {
+      "assay_name_reported": "Fe2+ Induced Polyreactivity to FVIII (Fe.FVIII.2)",
+      "assay_definition": "An assay measuring 'induced polyreactivity'. This is the binding of an antibody to Factor VIII (FVIII) protein after the antibody has been exposed to Fe2+ (iron). This indicates a change in binding profile upon oxidative stress. Higher binding is considered unfavorable.",
+      "readout": {
+        "primary_metric_name": "Induced FVIII Binding Score",
+        "raw_units": "Fe.FVIII.2",
+        "normalized_units": "FeFVIII",
+        "directionality": "lower_is_better",
+        "value_transformations": "The specific units or value transformation (e.g., fold-change, OD) are not specified in the main paper; they are likely in the original source publication."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1 (inferred from context of other assays in the paper)",
+        "concentration": "",
+        "buffer": "",
+        "pH": "",
+        "salt_or_additives": "Antibodies are exposed to Fe2+ to induce the polyreactive state.",
+        "temperature": "",
+        "incubation_or_stress": "Exposure to Fe2+."
+      },
+      "antigen_info": {
+        "antigen_used": "Factor VIII (FVIII) protein",
+        "binding_state": "",
+        "notes": "This assay measures binding to FVIII after inducement by an external stressor (Fe2+)."
+      },
+      "platform_and_instrumentation": {
+        "platform": "",
+        "instrument_vendor_model": "",
+        "columns_or_chips_or_surfaces": "",
+        "detection_mode": ""
+      },
+      "analysis_pipeline": {
+        "processing_steps": "",
+        "controls_and_standards": "",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": "The 90% threshold for the 50 approved mAbs in 2022 is 6.67 ± 0.55."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "This paper is a review article. The detailed experimental protocol for the induced polyreactivity assay is not included and is expected to be in the original source publication (likely reference 6, Lecerf et al., 2022).",
+        "Specifics of the readout (e.g., raw units, value transformation), antibody format, concentration, buffer, platform, and analysis pipeline are missing."
+      ],
+      "evidence": [
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "3",
+          "location": "Table 2",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "5",
+          "location": "Table 3",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "3",
+          "location": "Text body",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "assay_definition (details)",
+    "readout (value_transformations and raw units)",
+    "sample_and_format (most fields)",
+    "antigen_info (binding_state)",
+    "platform_and_instrumentation (all fields)",
+    "analysis_pipeline (most fields)",
+    "replicates_and_statistics (all fields)"
+  ]
+}

assay_metadata/flab2/jain2023identifying_FvLysM2_assay_metadata.txt

@@ -0,0 +1,80 @@
+{
+  "endpoint": "polyreactivity",
+  "assay_variants": [
+    {
+      "assay_name_reported": "Fe2+ Induced Polyreactivity to Lysozyme (Fe.LysM.2)",
+      "assay_definition": "An assay measuring 'induced polyreactivity'. This is the binding of an antibody to Lysozyme (LysM) protein after the antibody has been exposed to Fe2+ (iron). This indicates a change in binding profile upon oxidative stress. Higher binding is considered unfavorable.",
+      "readout": {
+        "primary_metric_name": "Induced Lysozyme Binding Score",
+        "raw_units": "Fe.LysM.2",
+        "normalized_units": "FeLysM",
+        "directionality": "lower_is_better",
+        "value_transformations": "The specific units or value transformation (e.g., fold-change, OD) are not specified in the main paper; they are likely in the original source publication."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1 (inferred from context of other assays in the paper)",
+        "concentration": "",
+        "buffer": "",
+        "pH": "",
+        "salt_or_additives": "Antibodies are exposed to Fe2+ to induce the polyreactive state.",
+        "temperature": "",
+        "incubation_or_stress": "Exposure to Fe2+."
+      },
+      "antigen_info": {
+        "antigen_used": "Lysozyme (LysM) protein",
+        "binding_state": "",
+        "notes": "This assay measures binding to Lysozyme after inducement by an external stressor (Fe2+)."
+      },
+      "platform_and_instrumentation": {
+        "platform": "",
+        "instrument_vendor_model": "",
+        "columns_or_chips_or_surfaces": "",
+        "detection_mode": ""
+      },
+      "analysis_pipeline": {
+        "processing_steps": "",
+        "controls_and_standards": "",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": "The 90% threshold for the 50 approved mAbs in 2022 is 8.27 ± 0.49."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "This paper is a review article. The detailed experimental protocol for the induced polyreactivity assay is not included and is expected to be in the original source publication (likely reference 6, Lecerf et al., 2022).",
+        "Specifics of the readout (e.g., raw units, value transformation), antibody format, concentration, buffer, platform, and analysis pipeline are missing."
+      ],
+      "evidence": [
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "3",
+          "location": "Table 2",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "5",
+          "location": "Table 3",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "3",
+          "location": "Text body",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "assay_definition (details)",
+    "readout (value_transformations and raw units)",
+    "sample_and_format (most fields)",
+    "antigen_info (binding_state)",
+    "platform_and_instrumentation (all fields)",
+    "analysis_pipeline (most fields)",
+    "replicates_and_statistics (all fields)"
+  ]
+}

assay_metadata/flab2/jain2023identifying_HEPRT3_assay_metadata.txt

@@ -0,0 +1,85 @@
+{
+  "endpoint": "pharmacokinetics",
+  "assay_variants": [
+    {
+      "assay_name_reported": "Heparin Column Retention Time",
+      "assay_definition": "This is an in vitro affinity chromatography assay that measures the retention time (RT) of an antibody on a heparin-functionalized column. This assay serves as an in vitro surrogate to predict in vivo clearance. Increased retention time, indicating stronger binding to the negatively charged heparin, is considered a proxy for non-specific interactions with the cell surface glycocalyx that can lead to faster clearance via pinocytosis.",
+      "readout": {
+        "primary_metric_name": "Retention Time (Hep RT)",
+        "raw_units": "Hep.RT.3",
+        "normalized_units": "HepRT",
+        "directionality": "lower_is_better",
+        "value_transformations": "The direct retention time is the reported metric."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "Not specified",
+        "buffer": "Not specified",
+        "pH": "Not specified",
+        "salt_or_additives": "Not specified",
+        "temperature": "Not specified",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "no antigen/target context mentioned",
+        "binding_state": "",
+        "notes": "This assay measures binding to heparin, which is a surrogate for charge-based interactions, not the therapeutic target of the antibodies."
+      },
+      "platform_and_instrumentation": {
+        "platform": "Affinity Chromatography (likely HPLC)",
+        "instrument_vendor_model": "Not specified",
+        "columns_or_chips_or_surfaces": "Heparin column",
+        "detection_mode": "Not specified (likely UV absorbance)"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "The retention time of each antibody on the heparin column is measured and reported.",
+        "controls_and_standards": "Not specified",
+        "qc_criteria": "Not specified",
+        "reported_thresholds_or_bins": "A 90% threshold for approved antibodies was calculated to be 0.84 +/- 0.05."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "The paper does not report direct in vivo pharmacokinetics data (e.g., clearance, half-life). It reports results from an in vitro heparin binding assay which is a surrogate for PK.",
+        "The '.3' suffix in 'Hep.RT.3' likely refers to the data's literature source as mapped in the paper's correlation matrix (Figure 1), not a direct parameter of the assay itself."
+      ],
+      "evidence": [
+        {
+          "source_file": "kmab_a_2200540_sm7528.docx",
+          "page": "",
+          "location": "Definitions",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "3",
+          "location": "Table 2",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "3",
+          "location": "Results, paragraph 3",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "5",
+          "location": "Table 3",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "instrument_vendor_model",
+    "column details (vendor, type)",
+    "buffer conditions (pH, salt)",
+    "detection_mode",
+    "controls_and_standards",
+    "n_replicates"
+  ]
+}

assay_metadata/flab2/jain2023identifying_Heme2_assay_metadata.txt

@@ -0,0 +1,80 @@
+{
+  "endpoint": "polyreactivity",
+  "assay_variants": [
+    {
+      "assay_name_reported": "Heme Binding Assay (Heme.2)",
+      "assay_definition": "An assay measuring polyreactivity to the cofactor Heme. It is clustered with Folate binding and Heparin Retention Time, and considered a proxy for polyreactivity. Higher binding is considered unfavorable.",
+      "readout": {
+        "primary_metric_name": "Heme Binding Score",
+        "raw_units": "Heme.2",
+        "normalized_units": "Heme",
+        "directionality": "lower_is_better",
+        "value_transformations": "The specific units or value transformation (e.g., fold-change, OD) are not specified in the main paper; they are likely in the original source publication."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1 (inferred from context of other assays in the paper)",
+        "concentration": "",
+        "buffer": "",
+        "pH": "",
+        "salt_or_additives": "",
+        "temperature": "",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "Heme",
+        "binding_state": "",
+        "notes": "This assay measures binding to the cofactor heme."
+      },
+      "platform_and_instrumentation": {
+        "platform": "",
+        "instrument_vendor_model": "",
+        "columns_or_chips_or_surfaces": "",
+        "detection_mode": ""
+      },
+      "analysis_pipeline": {
+        "processing_steps": "",
+        "controls_and_standards": "",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": "The 90% threshold for the 48 approved mAbs in 2022 is 10.73 ± 3.50."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "This paper is a review article. The detailed experimental protocol for the Heme binding assay is not included and is expected to be in the original source publication (likely reference 7, Lecerf et al., 2021).",
+        "Specifics of the readout (e.g., raw units, value transformation), antibody format, concentration, buffer, platform, and analysis pipeline are missing."
+      ],
+      "evidence": [
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "3",
+          "location": "Table 2",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "5",
+          "location": "Table 3",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "3",
+          "location": "Text body",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "assay_definition (details)",
+    "readout (value_transformations and raw units)",
+    "sample_and_format (all fields)",
+    "antigen_info (binding_state)",
+    "platform_and_instrumentation (all fields)",
+    "analysis_pipeline (most fields)",
+    "replicates_and_statistics (all fields)"
+  ]
+}

assay_metadata/flab2/jain2023identifying_HemeC32_assay_metadata.txt

@@ -0,0 +1,80 @@
+{
+  "endpoint": "polyreactivity",
+  "assay_variants": [
+    {
+      "assay_name_reported": "Heme-Induced Polyreactivity to C3 (Heme.C3.2)",
+      "assay_definition": "An assay measuring 'induced polyreactivity'. This is the binding of an antibody to Complement C3 protein after the antibody has been exposed to Heme. This indicates a change in binding profile upon oxidative stress. Higher binding is considered unfavorable.",
+      "readout": {
+        "primary_metric_name": "Induced C3 Binding Score",
+        "raw_units": "Heme.C3.2",
+        "normalized_units": "HemeC3",
+        "directionality": "lower_is_better",
+        "value_transformations": "The specific units or value transformation (e.g., fold-change, OD) are not specified in the main paper; they are likely in the original source publication."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1 (inferred from context of other assays in the paper)",
+        "concentration": "",
+        "buffer": "",
+        "pH": "",
+        "salt_or_additives": "Antibodies are exposed to Heme to induce the polyreactive state.",
+        "temperature": "",
+        "incubation_or_stress": "Exposure to Heme."
+      },
+      "antigen_info": {
+        "antigen_used": "Complement C3 protein",
+        "binding_state": "",
+        "notes": "This assay measures binding to C3 after inducement by an external stressor (Heme)."
+      },
+      "platform_and_instrumentation": {
+        "platform": "",
+        "instrument_vendor_model": "",
+        "columns_or_chips_or_surfaces": "",
+        "detection_mode": ""
+      },
+      "analysis_pipeline": {
+        "processing_steps": "",
+        "controls_and_standards": "",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": "The 90% threshold for the 48 approved mAbs in 2022 is 7.36 ± 0.78."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "This paper is a review article. The detailed experimental protocol for the induced polyreactivity assay is not included and is expected to be in the original source publication (likely reference 7, Lecerf et al., 2021).",
+        "Specifics of the readout (e.g., raw units, value transformation), antibody format, concentration, buffer, platform, and analysis pipeline are missing."
+      ],
+      "evidence": [
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "3",
+          "location": "Table 2",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "5",
+          "location": "Table 3",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "3",
+          "location": "Text body",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "assay_definition (details)",
+    "readout (value_transformations and raw units)",
+    "sample_and_format (most fields)",
+    "antigen_info (binding_state)",
+    "platform_and_instrumentation (all fields)",
+    "analysis_pipeline (most fields)",
+    "replicates_and_statistics (all fields)"
+  ]
+}

assay_metadata/flab2/jain2023identifying_HemeFVIII2_assay_metadata.txt

@@ -0,0 +1,80 @@
+{
+  "endpoint": "polyreactivity",
+  "assay_variants": [
+    {
+      "assay_name_reported": "Heme-Induced Polyreactivity to FVIII (Heme.FVIII.2)",
+      "assay_definition": "An assay measuring 'induced polyreactivity'. This is the binding of an antibody to Factor VIII (FVIII) protein after the antibody has been exposed to Heme. This indicates a change in binding profile upon oxidative stress. Higher binding is considered unfavorable.",
+      "readout": {
+        "primary_metric_name": "Induced FVIII Binding Score",
+        "raw_units": "Heme.FVIII.2",
+        "normalized_units": "HemeFVIII",
+        "directionality": "lower_is_better",
+        "value_transformations": "The specific units or value transformation (e.g., fold-change, OD) are not specified in the main paper; they are likely in the original source publication."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1 (inferred from context of other assays in the paper)",
+        "concentration": "",
+        "buffer": "",
+        "pH": "",
+        "salt_or_additives": "Antibodies are exposed to Heme to induce the polyreactive state.",
+        "temperature": "",
+        "incubation_or_stress": "Exposure to Heme."
+      },
+      "antigen_info": {
+        "antigen_used": "Factor VIII (FVIII) protein",
+        "binding_state": "",
+        "notes": "This assay measures binding to FVIII after inducement by an external stressor (Heme)."
+      },
+      "platform_and_instrumentation": {
+        "platform": "",
+        "instrument_vendor_model": "",
+        "columns_or_chips_or_surfaces": "",
+        "detection_mode": ""
+      },
+      "analysis_pipeline": {
+        "processing_steps": "",
+        "controls_and_standards": "",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": "The 90% threshold for the 48 approved mAbs in 2022 is 5.87 ± 0.72."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "This paper is a review article. The detailed experimental protocol for the induced polyreactivity assay is not included and is expected to be in the original source publication (likely reference 7, Lecerf et al., 2021).",
+        "Specifics of the readout (e.g., raw units, value transformation), antibody format, concentration, buffer, platform, and analysis pipeline are missing."
+      ],
+      "evidence": [
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "3",
+          "location": "Table 2",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "5",
+          "location": "Table 3",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "3",
+          "location": "Text body",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "assay_definition (details)",
+    "readout (value_transformations and raw units)",
+    "sample_and_format (most fields)",
+    "antigen_info (binding_state)",
+    "platform_and_instrumentation (all fields)",
+    "analysis_pipeline (most fields)",
+    "replicates_and_statistics (all fields)"
+  ]
+}

assay_metadata/flab2/jain2023identifying_HemeLysM2_assay_metadata.txt

@@ -0,0 +1,80 @@
+{
+  "endpoint": "polyreactivity",
+  "assay_variants": [
+    {
+      "assay_name_reported": "Heme-Induced Polyreactivity to Lysozyme (Heme.LysM.2)",
+      "assay_definition": "An assay measuring 'induced polyreactivity'. This is the binding of an antibody to Lysozyme (LysM) protein after the antibody has been exposed to Heme. This indicates a change in binding profile upon oxidative stress. Higher binding is considered unfavorable.",
+      "readout": {
+        "primary_metric_name": "Induced Lysozyme Binding Score",
+        "raw_units": "Heme.LysM.2",
+        "normalized_units": "HemeLysM",
+        "directionality": "lower_is_better",
+        "value_transformations": "The specific units or value transformation (e.g., fold-change, OD) are not specified in the main paper; they are likely in the original source publication."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1 (inferred from context of other assays in the paper)",
+        "concentration": "",
+        "buffer": "",
+        "pH": "",
+        "salt_or_additives": "Antibodies are exposed to Heme to induce the polyreactive state.",
+        "temperature": "",
+        "incubation_or_stress": "Exposure to Heme."
+      },
+      "antigen_info": {
+        "antigen_used": "Lysozyme (LysM) protein",
+        "binding_state": "",
+        "notes": "This assay measures binding to Lysozyme after inducement by an external stressor (Heme)."
+      },
+      "platform_and_instrumentation": {
+        "platform": "",
+        "instrument_vendor_model": "",
+        "columns_or_chips_or_surfaces": "",
+        "detection_mode": ""
+      },
+      "analysis_pipeline": {
+        "processing_steps": "",
+        "controls_and_standards": "",
+        "qc_criteria": "",
+        "reported_thresholds_or_bins": "The 90% threshold for the 48 approved mAbs in 2022 is 10.10 ± 1.36."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "",
+        "error_bars": "",
+        "stat_tests": ""
+      },
+      "notes_on_ambiguity": [
+        "This paper is a review article. The detailed experimental protocol for the induced polyreactivity assay is not included and is expected to be in the original source publication (likely reference 7, Lecerf et al., 2021).",
+        "Specifics of the readout (e.g., raw units, value transformation), antibody format, concentration, buffer, platform, and analysis pipeline are missing."
+      ],
+      "evidence": [
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "3",
+          "location": "Table 2",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "5",
+          "location": "Table 3",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches.pdf",
+          "page": "3",
+          "location": "Text body",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "assay_definition (details)",
+    "readout (value_transformations and raw units)",
+    "sample_and_format (most fields)",
+    "antigen_info (binding_state)",
+    "platform_and_instrumentation (all fields)",
+    "analysis_pipeline (most fields)",
+    "replicates_and_statistics (all fields)"
+  ]
+}

assay_metadata/flab2/jain2024assessment_ACSINS_assay_metadata.txt

@@ -0,0 +1,73 @@
+{
+  "endpoint": "self-aggregation",
+  "assay_variants": [
+    {
+      "assay_name_reported": "AC-SINS (Affinity-capture self-interaction nanoparticle spectroscopy)",
+      "assay_definition": "Measures the propensity of an antibody to self-interact by incubating it with gold nanoparticles coated with a capture reagent. Self-interaction causes the nanoparticles to agglomerate, resulting in a measurable shift in the plasmon wavelength.",
+      "readout": {
+        "primary_metric_name": "Wavelength Shift",
+        "raw_units": "AC-SINS delta lambda max (nm)",
+        "normalized_units": "ACSINS",
+        "directionality": "lower_is_better",
+        "value_transformations": "The readout is the raw wavelength shift in nanometers compared to a PBS control. No transformations are mentioned."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "0.02 mg/mL",
+        "buffer": "Antibodies were buffer-exchanged into 10 mM His-HCl, pH 6.0. The assay control is a PBS sample.",
+        "pH": "6.0",
+        "salt_or_additives": "10 mM His-HCl",
+        "temperature": "Not specified (Assumed room temperature)",
+        "incubation_or_stress": "Incubated with nanoparticles for 2 hours."
+      },
+      "antigen_info": {
+        "antigen_used": "false",
+        "binding_state": "unbound",
+        "notes": "no antigen mentioned"
+      },
+      "platform_and_instrumentation": {
+        "platform": "Nanoparticle Spectroscopy",
+        "instrument_vendor_model": "Molecular Devices Spectra Max M2 with SoftMax Pro6 software",
+        "columns_or_chips_or_surfaces": "Gold nanoparticles (Ted Pella Inc.) coated to 80% capacity with anti-human goat IgG Fc (Jackson ImmunoResearch).",
+        "detection_mode": "UV-Vis Spectroscopy (plasmon wavelength)"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "The wavelength shift of the antibody sample is measured and compared to that of a control PBS sample. A higher shift indicates greater self-interaction.",
+        "controls_and_standards": "A PBS sample is used as a negative control.",
+        "qc_criteria": "Not specified",
+        "reported_thresholds_or_bins": "For selecting a diverse validation set, antibodies with 'large AC-SINS wavelength shifts (>13 nm)' were categorized as 'Positive' (i.e., having higher self-interaction and potential PK risk)."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Spearman rank correlation was used to correlate AC-SINS results with in vivo clearance (p = 0.55)."
+      },
+      "notes_on_ambiguity": [
+        "The temperature for the 2-hour incubation is not specified."
+      ],
+      "evidence": [
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "13",
+          "location": "Affinity-capture self-interaction nanoparticle spectroscopy",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "3",
+          "location": "Results",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "5",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "AC-SINS: Incubation Temperature"
+  ]
+}

assay_metadata/flab2/jain2024assessment_CIC_assay_metadata.txt

@@ -0,0 +1,74 @@
+{
+  "endpoint": "self-aggregation",
+  "assay_variants": [
+    {
+      "assay_name_reported": "CIC (Cross-Interaction Chromatography)",
+      "assay_definition": "Measures non-specific cross-interaction by passing an antibody over a column where polyclonal human IgG has been immobilized. The retention time on this column, relative to a control column, indicates the antibody's propensity for non-specific protein-protein interactions.",
+      "readout": {
+        "primary_metric_name": "k' (retention factor)",
+        "raw_units": "CIC Column K",
+        "normalized_units": "CIC",
+        "directionality": "lower_is_better",
+        "value_transformations": "The retention factor k' is calculated as (Tr - Tm) / Tm, where Tr is the retention time on the IgG-coupled column and Tm is the retention time on a control column."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG",
+        "concentration": "0.5 mg/mL",
+        "buffer": "PBS",
+        "pH": "7.4",
+        "salt_or_additives": "Standard PBS salts.",
+        "temperature": "Not specified (Assumed ambient)",
+        "incubation_or_stress": "The assay is a chromatographic separation at a flow rate of 0.1 mL/min."
+      },
+      "antigen_info": {
+        "antigen_used": "false",
+        "binding_state": "unbound",
+        "notes": "no antigen mentioned"
+      },
+      "platform_and_instrumentation": {
+        "platform": "Column Chromatography",
+        "instrument_vendor_model": "Thermo Scientific Vanquish System",
+        "columns_or_chips_or_surfaces": "Hi-Trap NHS-activated column coupled with purified IgGs from human serum.",
+        "detection_mode": "UV detector (224 nm and 280 nm)"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "The retention time (RT) of the antibody peak is determined on both the test (polyclonal IgG) column and a control (empty) column. The retention factor k' is calculated from these two values.",
+        "controls_and_standards": "A control column is generated in parallel without coupled antibody to determine the void retention time (Tm).",
+        "qc_criteria": "Not specified",
+        "reported_thresholds_or_bins": "No specific threshold is reported for this assay."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Spearman rank correlation was used to correlate CIC results with in vivo clearance (p = 0.59)."
+      },
+      "notes_on_ambiguity": [
+        "The assay temperature is not specified.",
+        "There is a discrepancy in the protein concentration mentioned between Table 1 (0.75 mg/mL) and the methods section (0.5 mg/mL). The methods section value is used here."
+      ],
+      "evidence": [
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "14",
+          "location": "Cross interaction column chromatography",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "14",
+          "location": "Cross interaction column chromatography",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "5",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "CIC: Assay Temperature"
+  ]
+}

assay_metadata/flab2/jain2024assessment_CSSINS_assay_metadata.txt

@@ -0,0 +1,73 @@
+{
+  "endpoint": "self-aggregation",
+  "assay_variants": [
+    {
+      "assay_name_reported": "CS-SINS (Charged-Stabilized Self-Interaction Nanoparticle Spectroscopy)",
+      "assay_definition": "Measures antibody self-interaction, likely under conditions that probe charge-based interactions. The paper provides very limited detail on the method, citing other literature. It is categorized as a general developability/manufacturability assay.",
+      "readout": {
+        "primary_metric_name": "CS-SINS score",
+        "raw_units": "CS-SINS (ave)",
+        "normalized_units": "CSSINS",
+        "directionality": "not_specified",
+        "value_transformations": "Not specified. The readout is referred to as a 'score'."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG",
+        "concentration": "1 mg/mL",
+        "buffer": "Not specified",
+        "pH": "Not specified",
+        "salt_or_additives": "Not specified",
+        "temperature": "Not specified",
+        "incubation_or_stress": "Not specified"
+      },
+      "antigen_info": {
+        "antigen_used": "false",
+        "binding_state": "unbound",
+        "notes": "no antigen mentioned"
+      },
+      "platform_and_instrumentation": {
+        "platform": "The format is listed as 'ELISA' in Table 1, suggesting it is performed in a microplate, but the assay name implies nanoparticle spectroscopy.",
+        "instrument_vendor_model": "Not specified",
+        "columns_or_chips_or_surfaces": "Not specified, but expected to use nanoparticles.",
+        "detection_mode": "Not specified, inferred to be UV-Vis Spectroscopy."
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Not specified",
+        "controls_and_standards": "Not specified",
+        "qc_criteria": "Not specified",
+        "reported_thresholds_or_bins": "No specific threshold is reported for this assay."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Spearman rank correlation was used to correlate CS-SINS results with in vivo clearance (p = -0.01)."
+      },
+      "notes_on_ambiguity": [
+        "The paper does not provide a detailed method for the CS-SINS assay, citing reference 19 instead. Consequently, most experimental details are missing.",
+        "Table 1 lists the format as 'ELISA', which is atypical for a SINS (spectroscopy) assay, creating ambiguity about the exact platform."
+      ],
+      "evidence": [
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "3",
+          "location": "Biophysical characterization of the diverse subset selected",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "5",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "CS-SINS: buffer",
+    "CS-SINS: pH",
+    "CS-SINS: incubation/stress conditions",
+    "CS-SINS: instrument model",
+    "CS-SINS: surface chemistry",
+    "CS-SINS: analysis pipeline details"
+  ]
+}

assay_metadata/flab2/jain2024assessment_Fab_pI_assay_metadata.txt

@@ -0,0 +1,74 @@
+{
+  "endpoint": "self-aggregation",
+  "assay_variants": [
+    {
+      "assay_name_reported": "Fab pI (Fab Isoelectric Point)",
+      "assay_definition": "The isoelectric point (pI) of the Fab fragment is a computationally derived physicochemical property. It reflects the overall charge of the molecule, which can influence various developability attributes, including aggregation propensity and pharmacokinetics.",
+      "readout": {
+        "primary_metric_name": "Isoelectric Point (pI)",
+        "raw_units": "Fab.pI",
+        "normalized_units": "pI",
+        "directionality": "depends",
+        "value_transformations": "The pI value is a direct calculation from the protein sequence and is unitless."
+      },
+      "sample_and_format": {
+        "molecule_format": "Fab fragment (derived from IgG1 sequence)",
+        "concentration": "In silico calculation",
+        "buffer": "Not applicable (in silico)",
+        "pH": "The pI itself is a pH value, not measured in a specific buffer.",
+        "salt_or_additives": "Not applicable (in silico)",
+        "temperature": "Not applicable (in silico)",
+        "incubation_or_stress": "Not applicable (in silico)"
+      },
+      "antigen_info": {
+        "antigen_used": "false",
+        "binding_state": "unbound",
+        "notes": "Fab pI is a calculated property of the antibody itself, independent of antigen."
+      },
+      "platform_and_instrumentation": {
+        "platform": "In silico calculation",
+        "instrument_vendor_model": "Not specified (computational tool)",
+        "columns_or_chips_or_surfaces": "Not applicable",
+        "detection_mode": "Not applicable"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "The Fab pI is calculated directly from the amino acid sequence of the Fab fragment. Details for the calculation are referenced as Supplementary Information.",
+        "controls_and_standards": "Not applicable",
+        "qc_criteria": "Not specified",
+        "reported_thresholds_or_bins": "Extreme pI values (both low and high) have been associated with poor PK outcomes. Specific pass/fail thresholds are not explicitly defined in the paper's text, but rather broad ranges or distributions are considered."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not applicable",
+        "error_bars": "Not applicable",
+        "stat_tests": "Spearman rank correlation was used to assess correlation with in vivo clearance (p = 0.23)."
+      },
+      "notes_on_ambiguity": [
+        "While Fab pI is a key biophysical property, its direct relationship to 'self-aggregation' is often indirect, correlating as a risk factor rather than a direct aggregation measurement.",
+        "The specific software or algorithm used for pI calculation is not mentioned in the main text."
+      ],
+      "evidence": [
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "3",
+          "location": "Results",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "5",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "13",
+          "location": "Materials and methods",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "Fab pI: Specific software/algorithm for calculation not specified"
+  ]
+}

assay_metadata/flab2/jain2024assessment_FcRn_assay_metadata.txt

@@ -0,0 +1,88 @@
+{
+  "endpoint": "pharmacokinetics",
+  "assay_variants": [
+    {
+      "assay_name_reported": "FcRn cellular assay",
+      "assay_definition": "An in vitro, cell-based assay measuring the amount of antibody recycled by a stable human FcRn (huFCGRT)-expressing MDCKII cell line. The assay simulates the FcRn salvage pathway by loading antibodies onto the cells at acidic pH (6.0) for 2 hours, followed by a 24-hour release phase at physiological pH (7.4). The amount of antibody recycled into the supernatant is then quantified. This serves as an in vitro surrogate for in vivo half-life, where more efficient recycling predicts slower clearance.",
+      "readout": {
+        "primary_metric_name": "Concentration of recycled antibody",
+        "raw_units": "FcRn Cellular Recycling (ng/mL)",
+        "normalized_units": "FcRn recycling",
+        "directionality": "higher_is_better",
+        "value_transformations": "The final readout is the concentration of antibody (ng/mL) in the release media, normalized to the total protein amount as determined by BCA."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "20 µg/ml during the 2-hour loading phase.",
+        "buffer": "Loading buffer at pH 6.0; release media at pH 7.4.",
+        "pH": "6.0 (loading), 7.4 (release)",
+        "salt_or_additives": "Not specified",
+        "temperature": "37°C",
+        "incubation_or_stress": "2-hour loading incubation, followed by 24-hour release incubation."
+      },
+      "antigen_info": {
+        "antigen_used": "no antigen/target context mentioned",
+        "binding_state": "",
+        "notes": "This assay measures the interaction with the FcRn receptor, not the antibody's therapeutic target."
+      },
+      "platform_and_instrumentation": {
+        "platform": "Cell-based assay (MDCKII cells). The specific platform for quantifying the final antibody concentration (e.g., ELISA, MSD) is not specified.",
+        "instrument_vendor_model": "Not specified",
+        "columns_or_chips_or_surfaces": "96-well cell culture plate.",
+        "detection_mode": "Not specified"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Antibody concentration in the supernatant is measured after a 24-hour release period. The recycling rate is normalized to the protein amount determined by BCA.",
+        "controls_and_standards": "Not specified",
+        "qc_criteria": "Not specified",
+        "reported_thresholds_or_bins": ""
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "This is an in vitro functional assay, not a direct in vivo PK study.",
+        "The paper does not explicitly state the method used to quantify the final concentration of recycled antibody in ng/mL (e.g., ELISA, MSD), although this is a standard step in such assays. It only mentions using a BCA assay for normalization."
+      ],
+      "evidence": [
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "14",
+          "location": "Materials and methods, FcRn cellular assay",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "14",
+          "location": "Materials and methods, FcRn cellular assay",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "15",
+          "location": "Materials and methods, FcRn cellular assay",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "15",
+          "location": "Materials and methods, FcRn cellular assay",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "6",
+          "location": "Figure 3b",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "Quantification platform for recycled antibody (e.g., ELISA, MSD)",
+    "Controls and standards used",
+    "Number of replicates"
+  ]
+}

assay_metadata/flab2/jain2024assessment_HIC_assay_metadata.txt

@@ -0,0 +1,77 @@
+{
+  "endpoint": "self-aggregation",
+  "assay_variants": [
+    {
+      "assay_name_reported": "HIC (Hydrophobic Interaction Chromatography)",
+      "assay_definition": "Measures the relative hydrophobicity of an antibody by assessing its retention time on a hydrophobic column under a salt gradient. Longer retention times indicate higher hydrophobicity, which can correlate with increased aggregation propensity.",
+      "readout": {
+        "primary_metric_name": "Retention Time (RT)",
+        "raw_units": "HIC RT (min)",
+        "normalized_units": "HIC",
+        "directionality": "lower_is_better",
+        "value_transformations": "The readout is the retention time in minutes. No explicit transformations are described."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG",
+        "concentration": "1 mg/mL (sample concentration before spiking)",
+        "buffer": "Mobile phase A: 1.8 M ammonium sulfate, 0.1 M sodium phosphate; Mobile phase B: 0.1 M sodium phosphate.",
+        "pH": "6.5",
+        "salt_or_additives": "Ammonium sulfate (used to create hydrophobic interaction)",
+        "temperature": "Not specified (Assumed ambient)",
+        "incubation_or_stress": "Chromatographic separation involves a linear gradient elution over 20 minutes."
+      },
+      "antigen_info": {
+        "antigen_used": "false",
+        "binding_state": "unbound",
+        "notes": "HIC measures an intrinsic property of the antibody, not its interaction with an antigen."
+      },
+      "platform_and_instrumentation": {
+        "platform": "Column Chromatography",
+        "instrument_vendor_model": "Not explicitly specified (UV detector used)",
+        "columns_or_chips_or_surfaces": "Sepax Proteomix HIC butyl-NP5 column",
+        "detection_mode": "UV absorbance monitoring at 280 nm"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "5 µg of IgG sample (1 mg/mL) is spiked into mobile phase A to achieve a final ammonium sulfate concentration of approximately 1 M, then subjected to a linear gradient elution.",
+        "controls_and_standards": "Not specified",
+        "qc_criteria": "Not specified",
+        "reported_thresholds_or_bins": "No specific threshold is reported in this paper for HIC."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Spearman rank correlation coefficient of 0.39 with in vivo clearance."
+      },
+      "notes_on_ambiguity": [
+        "The instrument vendor and model are not explicitly stated, only the column details.",
+        "The assay temperature is not specified.",
+        "There is a discrepancy between the sample concentration of 1 mg/mL in the methods and 0.4 mg/mL listed in Table 1."
+      ],
+      "evidence": [
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "13",
+          "location": "Hydrophobic interaction chromatography",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "13",
+          "location": "Hydrophobic interaction chromatography",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "5",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "HIC: instrument vendor/model",
+    "HIC: assay temperature",
+    "HIC: QC criteria"
+  ]
+}

assay_metadata/flab2/jain2024assessment_Herapin_RT_assay_metadata.txt

@@ -0,0 +1,74 @@
+{
+  "endpoint": "polyreactivity",
+  "assay_variants": [
+    {
+      "assay_name_reported": "Heparin binding chromatography",
+      "assay_definition": "A chromatography-based assay that measures the retention time (RT) of an antibody on a heparin column. Heparin is a highly sulfated glycosaminoglycan, and binding to it is used as a surrogate for interactions with the negatively charged glycocalyx on endothelial cells, which can contribute to nonspecific clearance. A longer retention time indicates stronger interaction and is considered unfavorable.",
+      "readout": {
+        "primary_metric_name": "Relative Retention Time (RT)",
+        "raw_units": "Herapin Column Rel RT",
+        "normalized_units": "Herapin RT",
+        "directionality": "lower_is_better",
+        "value_transformations": "The retention time of the test mAb is normalized to the retention time of a reference mAb (adalimumab) to give a Relative_RT."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "1.75 mg/mL (5 µL injected)",
+        "buffer": "Mobile Phase A: Tris pH 7.4. Mobile Phase B: Tris 20 mM pH 7.4 with 1 M NaCl.",
+        "pH": "7.4",
+        "salt_or_additives": "A salt gradient from 0 to 0.55 M NaCl is used for elution.",
+        "temperature": "Not specified.",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "Heparin",
+        "binding_state": "Immobilized on a chromatography column.",
+        "notes": ""
+      },
+      "platform_and_instrumentation": {
+        "platform": "HPLC",
+        "instrument_vendor_model": "Thermo Scientific Vanquish System with UV detector",
+        "columns_or_chips_or_surfaces": "Heparin column (specific type not mentioned, but method adapted from Kraft et al., 2020)",
+        "detection_mode": "UV absorbance at 224 nm and 280 nm."
+      },
+      "analysis_pipeline": {
+        "processing_steps": "The retention time (RT) is defined as the elution time of the peak maximum, determined using Trace Finder software. The RT is then normalized to a reference standard.",
+        "controls_and_standards": "Adalimumab is used as a reference to verify system stability and to calculate relative RT.",
+        "qc_criteria": "Columns were equilibrated with at least 3 column volumes of PBS between runs.",
+        "reported_thresholds_or_bins": "No specific threshold is defined in this paper, but it is used in a multivariate model to predict clearance."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Spearman rank correlation was used to assess relationship with clearance."
+      },
+      "notes_on_ambiguity": [
+        "The specific vendor and type of the heparin column are not explicitly stated in this paper, only that the method was adapted from a prior publication."
+      ],
+      "evidence": [
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "14",
+          "location": "Heparin binding chromatography",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "14",
+          "location": "Heparin binding chromatography",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "5",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "temperature",
+    "replicates_and_statistics (n_replicates, error_bars)"
+  ]
+}

assay_metadata/flab2/jain2024assessment_PSR_assay_metadata.txt

@@ -0,0 +1,77 @@
+{
+  "endpoint": "polyreactivity",
+  "assay_variants": [
+    {
+      "assay_name_reported": "Polyspecificity reagent binding (PSR)",
+      "assay_definition": "A flow-cytometry based assay measuring the binding of yeast-displayed IgGs to a polyspecificity reagent (PSR). The PSR consists of biotinylated soluble membrane and cytosolic proteins from CHO cells. Binding is a measure of non-specific interactions, with higher binding being unfavorable.",
+      "readout": {
+        "primary_metric_name": "Normalized polyspecificity score",
+        "raw_units": "PSR",
+        "normalized_units": "PSR",
+        "directionality": "lower_is_better",
+        "value_transformations": "Median fluorescence intensity (MFI) values from the R-PE channel were normalized from 0 to 1 based on three reference antibodies exhibiting low, medium, and high PSR MFI values."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG-presenting yeast",
+        "concentration": "Not specified",
+        "buffer": "Not specified",
+        "pH": "Not specified",
+        "salt_or_additives": "Secondary labeling mix included Extravidin-R-PE, anti-human LC-FITC, and propidium iodide.",
+        "temperature": "Not specified",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "Polyspecificity Reagent (PSR)",
+        "binding_state": "Soluble",
+        "notes": "PSR was generated from soluble membrane and cytosolic proteins prepared from CHO cells, which were then biotinylated using NHS-LC-Biotin."
+      },
+      "platform_and_instrumentation": {
+        "platform": "Flow Cytometry (FACS)",
+        "instrument_vendor_model": "FACS Canto (BD Biosciences) with an HTS sample injector",
+        "columns_or_chips_or_surfaces": "",
+        "detection_mode": "Median fluorescence intensity (MFI) in the R-PE channel."
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Yeast-displayed IgGs were incubated with the PSR, washed, and then incubated with a secondary labeling mix. The MFI was measured by flow cytometry.",
+        "controls_and_standards": "Three reference antibodies exhibiting low, medium, and high PSR MFI values were used for normalization.",
+        "qc_criteria": "Not specified",
+        "reported_thresholds_or_bins": "A threshold of >0.75 was used to select for antibodies in the 'Positive' category for high non-specific binding."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Spearman rank correlation was used to assess relationship with clearance."
+      },
+      "notes_on_ambiguity": [
+        "The specific buffers and incubation times/temperatures are not detailed in the methods.",
+        "The identity of the three reference antibodies used for normalization is not disclosed."
+      ],
+      "evidence": [
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "13",
+          "location": "Polyspecificity reagent binding",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "3",
+          "location": "Results",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "5",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "incubation_or_stress (time)",
+    "temperature",
+    "buffer",
+    "replicates_and_statistics (n_replicates, error_bars)"
+  ]
+}

assay_metadata/flab2/jain2024assessment_SEC_assay_metadata.txt

@@ -0,0 +1,79 @@
+{
+  "endpoint": "self-aggregation",
+  "assay_variants": [
+    {
+      "assay_name_reported": "SEC (Size Exclusion Chromatography)",
+      "assay_definition": "Directly measures the level of aggregation in an antibody sample by separating molecules based on size. The primary readout is the percentage of the sample that exists as a monomer.",
+      "readout": {
+        "primary_metric_name": "% Monomer",
+        "raw_units": "SEC % Monomer",
+        "normalized_units": "SEC",
+        "directionality": "higher_is_better",
+        "value_transformations": "The readout is a direct percentage calculated from the chromatogram peak areas."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG",
+        "concentration": "0.5 mg/mL",
+        "buffer": "Not specified",
+        "pH": "Not specified",
+        "salt_or_additives": "Not specified",
+        "temperature": "Not specified",
+        "incubation_or_stress": "This is a quality control measurement on the final sample, not an accelerated stability study. A polishing step was used to ensure samples were >95% monomeric."
+      },
+      "antigen_info": {
+        "antigen_used": "false",
+        "binding_state": "unbound",
+        "notes": "SEC measures an intrinsic property of the antibody preparation."
+      },
+      "platform_and_instrumentation": {
+        "platform": "Column Chromatography",
+        "instrument_vendor_model": "Not specified",
+        "columns_or_chips_or_surfaces": "Not specified",
+        "detection_mode": "Not specified (inferred to be UV absorbance)"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Not specified, but standard analysis involves integrating the area of the monomer peak and dividing by the total area of all peaks.",
+        "controls_and_standards": "Not specified",
+        "qc_criteria": "The antibody production process included a polishing step to ensure final samples were >95% monomeric as assessed by SEC.",
+        "reported_thresholds_or_bins": "A threshold of >95% monomer was used as a quality control step during antibody production."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Spearman rank correlation with in vivo clearance was 0.11."
+      },
+      "notes_on_ambiguity": [
+        "The paper lacks a specific materials and methods section for SEC analysis, so most experimental details (e.g., buffer, column, instrument, temperature) are missing."
+      ],
+      "evidence": [
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "5",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "3",
+          "location": "Biophysical characterization of the diverse subset selected",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "13",
+          "location": "Antibody production in mammalian CHO cells",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "SEC: Buffer",
+    "SEC: pH",
+    "SEC: Temperature",
+    "SEC: Instrument Model",
+    "SEC: Column Details",
+    "SEC: Detection Mode",
+    "SEC: Analysis Details"
+  ]
+}

assay_metadata/flab2/jain2024assessment_Tm_assay_metadata.txt

@@ -0,0 +1,85 @@
+{
+  "endpoint": "thermostability",
+  "assay_variants": [
+    {
+      "assay_name_reported": "DSF Fab Tm",
+      "assay_definition": "Measurement of the melting temperature (Tm) of the antigen-binding fragment (Fab) domain using differential scanning fluorimetry (DSF). This assesses the thermal stability of the Fab domain.",
+      "readout": {
+        "primary_metric_name": "Fab Tm",
+        "raw_units": "Fab Tm by DSF (degreeC)",
+        "normalized_units": "DSF",
+        "directionality": "higher_is_better",
+        "value_transformations": "The primary metric is the direct melting temperature. No transformations are mentioned."
+      },
+      "sample_and_format": {
+        "molecule_format": "Fab and full-length mAb (IgG1)",
+        "concentration": "0.2-1 mg/mL",
+        "buffer": "10 mM His-HCl",
+        "pH": "6.0",
+        "salt_or_additives": "SYPRO Orange dye was added.",
+        "temperature": "Not specified",
+        "incubation_or_stress": "A thermal ramp from 40°C to 95°C was applied."
+      },
+      "antigen_info": {
+        "antigen_used": "false",
+        "binding_state": "unbound",
+        "notes": "No antigen mentioned in the DSF protocol."
+      },
+      "platform_and_instrumentation": {
+        "platform": "Differential Scanning Fluorimetry (DSF)",
+        "instrument_vendor_model": "BioRad CFX96 RT-PCR instrument",
+        "columns_or_chips_or_surfaces": "RT-PCR plate",
+        "detection_mode": "Fluorescence of SYPRO Orange dye."
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Tm was determined from the negative of the first derivative of the raw fluorescence data versus temperature.",
+        "controls_and_standards": "Not specified",
+        "qc_criteria": "Not specified",
+        "reported_thresholds_or_bins": "Not specified"
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Not specified"
+      },
+      "notes_on_ambiguity": [
+        "The precise heating rate in °C/min is not explicitly stated, only the temperature increments (0.5°C) and equilibration time (2 min).",
+        "The final concentration of SYPRO Orange dye in the assay is not specified, only that 10 µL of a 20x stock was used.",
+        "The sample volume is mentioned as 20uL, to which 10uL of dye is added, making a total of 30uL."
+      ],
+      "evidence": [
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "3",
+          "location": "Results, Selection of a validation dataset...",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "5",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "13",
+          "location": "Materials and methods, Differential scanning fluorimetry",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "13",
+          "location": "Materials and methods, Antibody production in mammalian CHO cells",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "Heating rate in °C/min",
+    "Final concentration of SYPRO Orange dye",
+    "Number of replicates",
+    "QC criteria for data acceptance",
+    "Details on baseline subtraction or curve fitting models"
+  ]
+}

assay_metadata/flab2/jain2024assessment_cIEF_assay_metadata.txt

@@ -0,0 +1,72 @@
+{
+  "endpoint": "self-aggregation",
+  "assay_variants": [
+    {
+      "assay_name_reported": "cIEF (Capillary Isoelectric Focusing)",
+      "assay_definition": "Measures the isoelectric point (pI) of the main antibody species. This technique separates proteins based on their charge, providing insights into charge heterogeneity, which can be an indicator of stability and aggregation propensity.",
+      "readout": {
+        "primary_metric_name": "Main peak pI",
+        "raw_units": "cIEF Main peak",
+        "normalized_units": "cIEF",
+        "directionality": "not_specified",
+        "value_transformations": "The readout is the isoelectric point value of the main peak, which is unitless."
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG",
+        "concentration": "1 mg/mL",
+        "buffer": "Not specified",
+        "pH": "Not specified (the assay measures pI, which is a pH value)",
+        "salt_or_additives": "Not specified",
+        "temperature": "Not specified",
+        "incubation_or_stress": "Not specified"
+      },
+      "antigen_info": {
+        "antigen_used": "false",
+        "binding_state": "unbound",
+        "notes": "cIEF measures an intrinsic physicochemical property of the antibody molecule."
+      },
+      "platform_and_instrumentation": {
+        "platform": "Capillary Electrophoresis",
+        "instrument_vendor_model": "Not specified",
+        "columns_or_chips_or_surfaces": "Not specified (uses a capillary)",
+        "detection_mode": "Not specified"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "Not specified, but involves separation of protein isoforms based on pI and quantification of the main peak.",
+        "controls_and_standards": "Not specified",
+        "qc_criteria": "Not specified",
+        "reported_thresholds_or_bins": "No specific thresholds or binning definitions are reported for cIEF main peak."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "Not specified",
+        "error_bars": "Not specified",
+        "stat_tests": "Spearman rank correlation coefficient of 0.26 with in vivo clearance."
+      },
+      "notes_on_ambiguity": [
+        "A detailed methods section for cIEF is not provided in the paper, leading to many missing experimental details (e.g., buffer composition, instrument type, detection method)."
+      ],
+      "evidence": [
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "3",
+          "location": "Biophysical characterization of the diverse subset selected",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "5",
+          "location": "Table 1",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": [
+    "cIEF: Buffer",
+    "cIEF: Temperature",
+    "cIEF: Instrument Model",
+    "cIEF: Column/Capillary Details",
+    "cIEF: Detection Mode",
+    "cIEF: Analysis Details"
+  ]
+}

assay_metadata/flab2/jain2024assessment_tg32_clearance_assay_metadata.txt

@@ -0,0 +1,87 @@
+{
+  "endpoint": "pharmacokinetics",
+  "assay_variants": [
+    {
+      "assay_name_reported": "In vivo pharmacokinetic evaluation in hFcRn Tg32 mice",
+      "assay_definition": "An in vivo pharmacokinetic (PK) study in human FcRn transgenic (hFcRn Tg32) mice to determine the in vivo disposition and clearance of 43 different IgG1 antibodies. The primary reported endpoint is linear clearance (CL), calculated from serum concentration-time profiles following a single intravenous dose.",
+      "readout": {
+        "primary_metric_name": "Clearance (CL)",
+        "raw_units": "Tg32 Clearance (ml/h/kg)",
+        "normalized_units": "Tg32 clearance",
+        "directionality": "lower_is_better",
+        "value_transformations": ""
+      },
+      "sample_and_format": {
+        "molecule_format": "IgG1",
+        "concentration": "5 mg/kg dose",
+        "buffer": "10 mM His-HCl, pH 6.0 buffer",
+        "pH": "",
+        "salt_or_additives": "",
+        "temperature": "",
+        "incubation_or_stress": ""
+      },
+      "antigen_info": {
+        "antigen_used": "Hen Egg Lysozyme (HEL)",
+        "binding_state": "The antibodies were raised against HEL, but the study was conducted in treatment-naïve mice. The paper explicitly states the antibodies are not cross-reactive to mouse targets and that Target-Mediated Drug Disposition (TMDD) is not anticipated.",
+        "notes": "The study was designed to measure non-specific, linear clearance."
+      },
+      "platform_and_instrumentation": {
+        "platform": "Immunocapture-Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS)",
+        "instrument_vendor_model": "Shimadzu HPLC with AB Sciex API7500 Qtrap",
+        "columns_or_chips_or_surfaces": "Ascentis® Express Peptide ES-C18 column (75×2.1 mm, ThermoFisher Scientific)",
+        "detection_mode": "Mass Spectrometry (MS/MS) of surrogate peptides"
+      },
+      "analysis_pipeline": {
+        "processing_steps": "PK parameters were estimated from individual animal data using non-compartmental analysis (NCA).",
+        "controls_and_standards": "Calibration range for quantification was 25-12800 ng/mL.",
+        "qc_criteria": "Concentration values below the limit of quantitation (BLQ) were set to 0. Profiles showing sharp drops typical of anti-drug antibody (ADA) interference were excluded.",
+        "reported_thresholds_or_bins": "A clearance value of 0.32 mL/h/kg was used as a threshold to distinguish between acceptable (slow) and fast clearance."
+      },
+      "replicates_and_statistics": {
+        "n_replicates": "n = 3 mice per antibody",
+        "error_bars": "Not specified",
+        "stat_tests": "Spearman rank correlation was used to assess relationships between in vitro measures and in vivo CL."
+      },
+      "notes_on_ambiguity": [],
+      "evidence": [
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "15",
+          "location": "Materials and methods, In vivo pharmacokinetic evaluation",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "15",
+          "location": "Materials and methods, In vivo pharmacokinetic evaluation",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "15",
+          "location": "Materials and methods, In vivo pharmacokinetic evaluation",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "8",
+          "location": "In vivo pharmacokinetic assessment",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "15",
+          "location": "Materials and methods, Bioanalytical quantification in plasma",
+          "quote_snippet_removed": true
+        },
+        {
+          "source_file": "Assessment and incorporation of in vitro correlates to pharmacokinetic outcomes in antibody developability workflows.pdf",
+          "page": "15",
+          "location": "Materials and methods, Bioanalytical quantification in plasma",
+          "quote_snippet_removed": true
+        }
+      ]
+    }
+  ],
+  "missing_fields_summary": []
+}