Update curated PROBE README documentation: data/embeddings/probe_protvec/README.md

data/embeddings/probe_protvec/README.md

@@ -1,40 +1,22 @@
-# probe_protvec_v1_1
+# Embedding name: PROBE-PROTVec
 
-Embedding ID: `probe_protvec`
-
-Former processing ID: `probe_protvec_v1_1`
+- Modality: Protein representation
+- Algorithm: Official PROBE human UniProt representation table, standardized by UniProt-to-master mapping
+- Embedding source URL: https://huggingface.co/spaces/HUBioDataLab/PROBE
+- Original model/code URL: https://github.com/HUBioDataLab/PROBE
 
 ## Public files
 
 - `embeddings.npz`: compressed NumPy archive containing the embedding matrix under key `embeddings`.
 - `genes.tsv`: row metadata table. Row order matches the embedding matrix.
 - `metadata.json`: machine-readable provenance and processing metadata.
-- `README.md`: this per-embedding documentation file.
 
 ## Matrix
 
-- Shape: `18873 genes × 100 dimensions`
+- Shape: `18,873 genes × 100 dimensions`
 - Dtype: `float32`
-- NPZ array key: `embeddings`
-
-The row order is authoritative:
-
-```text
-embeddings.npz['embeddings'][i, :]  corresponds to  genes.tsv row i
-```
 
-## Loading example
 
-```python
-import numpy as np
-import pandas as pd
-
-with np.load('embeddings.npz') as z:
-    X = z['embeddings']
-
-genes = pd.read_csv('genes.tsv', sep='\t')
-assert X.shape[0] == len(genes)
-```
 
 ## genes.tsv columns
 
@@ -44,36 +26,80 @@ assert X.shape[0] == len(genes)
 | `gene_symbol` | 18873 | 18873 | TSPAN6<br>TNMD<br>DPM1<br>SCYL3 | Gene symbol associated with the Ensembl gene ID. |
 | `gene_type` | 18873 | 1 | protein_coding | Gene biotype, usually protein_coding. |
 | `entrez_id` | 18870 | 18871 | 7105<br>64102<br>8813<br>57147 | NCBI Entrez Gene identifier, when available. |
-| `uniprot_id` | 18873 | 18873 | O43657<br>Q9H2S6<br>O60762<br>Q8IZE3 | UniProt accession or identifier, when available. |
+| `uniprot_id` | 18873 | 18873 | O43657<br>Q9H2S6<br>O60762<br>Q8IZE3 | UniProt accession or identifier matched from the PROBE source Entry accession. |
 | `canonical_transcript_id` | 18873 | 18873 | ENST00000373020<br>ENST00000373031<br>ENST00000371588<br>ENST00000367771 | Canonical transcript identifier recorded or used for this gene. |
 | `canonical_protein_id` | 18873 | 18873 | ENSP00000362111<br>ENSP00000362122<br>ENSP00000360644<br>ENSP00000356745 | Canonical protein identifier recorded or used for this gene. |
-| `source_embedding` | 18873 | 1 | PROBE_PROTVEC | Name of the original source embedding. |
-| `source_identifier_type` | 18873 | 1 | UniProt accession from PROBE Entry column | Type of source identifier used by the original embedding. |
-| `source_key_count` | 18873 | 3 | 1<br>2<br>4 | Number of source keys mapped or collapsed to this final gene. |
-| `source_keys_examples` | 18873 | 18873 | O43657<br>Q9H2S6<br>O60762<br>Q8IZE3 | Example source keys mapped to this final gene. |
-| `source_row_indices_examples` | 18873 | 18873 | 18377<br>17975<br>4793<br>12441 | Example source row indices mapped to this final gene. |
-| `mapping_methods` | 18873 | 1 | uniprot_accession_exact_unique | Mapping methods used to connect source records to the master gene table. |
-
-## Basic metadata
-
-| Field | Value |
-|---|---|
-| `modality` | protein sequence / protein representation from PROBE human UniProt archive |
-| `embedding_name` | probe_protvec_v1_1 |
-| `download_source` | Official PROBE human_representation_vectors.tar.gz archive from Zenodo record 5795850 plus official HUBioDataLab/PROBE repository |
-| `original_model_or_method` | PROTVEC |
-| `embedding_generated_by` | PROBE authors / original PROBE human representation archive |
+| `source_embedding` | 18873 | 1 | PROBE_PROTVEC | Name of the original PROBE source embedding. |
+| `source_identifier_type` | 18873 | 1 | UniProt accession from PROBE Entry column | Type of source identifier used by the original PROBE CSV file. |
+| `source_key_count` | 18873 | 3 | 1<br>2<br>4 | Number of PROBE UniProt source rows mapped or collapsed to this final master-table gene. |
+| `source_keys_examples` | 18873 | 18873 | O43657<br>Q9H2S6<br>O60762<br>Q8IZE3 | Example PROBE UniProt Entry accessions mapped to this final master-table gene. |
+| `source_row_indices_examples` | 18873 | 18873 | 18377<br>17975<br>4793<br>12441 | Example PROBE source row indices mapped to this final gene. |
+| `mapping_methods` | 18873 | 1 | uniprot_accession_exact_unique | Mapping methods used to connect PROBE UniProt Entry accessions to the master gene table. |
+
+
 
 ## Detailed processing notes
 
-TODO: manually paste and curate the processing explanation for this embedding from the central project README.
+### Source and interpretation
+
+This embedding is one PROBE human UniProt representation table standardized into the shared gene-embedding resource.
+
+This is a ProtVec protein representation from the PROBE archive.
+
+The source file used for this component was `PROTVEC_UNIPROT_HUMAN.csv` from the official PROBE human UniProt representation archive. The raw vectors were not regenerated locally. The local work here was identifier cleaning, UniProt-to-gene mapping, duplicate handling, QC, and conversion into the shared public resource format.
+
+### Provenance fields
+
+    source_name: PROBE-PROTVec
+    original_model_or_method: PROBE human UniProt representation archive
+    input_data_type: official PROBE human UniProt CSV representation table
+    input_source_file: PROTVEC_UNIPROT_HUMAN.csv
+    source_download_or_app_page: https://huggingface.co/spaces/HUBioDataLab/PROBE
+    source_code_page: https://github.com/HUBioDataLab/PROBE
+    raw_source_folder: ~/data/raw_embeddings/probe_official/human_representation_vectors/revision-1/
+    processing_script: ~/scripts/process_embeddings/process_probe_all_v1_1.py
+    preferred_batch_summary_report: ~/reports/mapping_reports/probe_all_v1_1_summary.tsv
+    source_identifier_type: UniProt Entry accession
+    mapping_identifier_type: UniProt accession matched to enriched master_gene_table.csv UniProt fields
+    source_rows_or_entries: 18,873 mapped source genes
+    final_mapped_genes: 18,873
+    model_or_feature_dimension: 100
+    training_or_finetuning: none
+    final_embedding_dtype: float32
+
+### Mapping and processing decisions
+
+Each PROBE CSV uses a UniProt accession in the `Entry` column. Source entries were cleaned to their canonical accession base by removing isoform suffixes when present.
+
+Cleaned UniProt accessions were mapped to master_gene_table.csv using `uniprot_id`, `hgnc_uniprot_ids`, and `map_uniprot_ids_all`. Only unique UniProt-to-master mappings were accepted. Ambiguous UniProt accessions were excluded. Duplicate source proteins mapping to the same final master-table gene were averaged within that gene.
+
+The exact underlying UniProt/protein sequence database snapshot is inherited from the PROBE archive and should be checked against the official PROBE release documentation if a strict sequence-database timestamp is required.
+
+### Processing workflow
+
+For this PROBE embedding:
+
+    1. Read `PROTVEC_UNIPROT_HUMAN.csv` from the PROBE human representation archive.
+    2. Use the `Entry` column as the source UniProt accession.
+    3. Remove isoform suffixes where present to obtain the canonical UniProt accession base.
+    4. Map source UniProt accessions to master_gene_table.csv through enriched UniProt fields.
+    5. Exclude unmapped and ambiguous UniProt accessions.
+    6. Average duplicate source rows only when they map to the same final master-table gene.
+    7. Save the final matrix as float32.
+
+### Important implementation decisions
+
+The PROBE vectors were taken directly from the official archive rather than recomputed. This keeps the PROBE batch aligned with the released human UniProt representation files.
+
+All PROBE embeddings use the same mapping logic, so differences between PROBE outputs reflect the source representation type rather than different gene-mapping rules.
 
-Please include, when relevant:
+### Summary of final mapping:
 
-- original source/model/checkpoint;
-- whether the embedding was downloaded or generated locally;
-- input data used;
-- identifier mapping and filtering decisions;
-- pooling, aggregation, PCA, or normalization method;
-- coverage and important caveats;
-- license or redistribution notes.
+    Source identifiers / source rows or entries: 18,873 mapped source genes
+    Dimensions: 100
+    Final mapped genes: 18,873
+    Master table rows: 20,097
+    Master coverage: 93.91%
+    Mapping strategy: UniProt Entry accession mapping through enriched master table
+    Ambiguous UniProt accessions: excluded
+    Duplicate final mappings averaged: yes