initial readme push

README.md

@@ -9,4 +9,105 @@ tags:
 - uniprot
 size_categories:
 - 100K<n<1M
----
+---
+# Dataset Card for PAIR
+
+This dataset contains all the text annotations we collected and parsed from UniProt Swiss-Prot February 2023 and used to train PAIR -- a simple framework to finetune protein language models using text annotations. You can read more details about PAIR here: https://www.biorxiv.org/content/10.1101/2024.07.22.604688v2.abstract
+
+## Dataset Details
+
+### Dataset Description
+
+<!-- Provide a longer summary of what this dataset is. -->
+
+
+### Dataset Sources
+
+- **Repository:** (coming soon!)
+- **Paper:** https://www.biorxiv.org/content/10.1101/2024.07.22.604688v2.abstract
+- **Model checkpoints:** https://huggingface.co/h4duan
+
+## Uses
+
+<!-- Address questions around how the dataset is intended to be used. -->
+
+### Direct Use
+
+<!-- This section describes suitable use cases for the dataset. -->
+
+
+### Out-of-Scope Use
+
+<!-- This section addresses misuse, malicious use, and uses that the dataset will not work well for. -->
+
+This dataset contains text annotations from Swiss-Prot February 2023; our models were trained on all of them. Please be mindful about potential data leakage from time splits/identical protein sequences on any downstream tasks in your setup.
+
+## Dataset Structure
+
+<!-- This section provides a description of the dataset fields, and additional information about the dataset structure such as criteria used to create the splits, relationships between data points, etc. -->
+
+[More Information Needed]
+
+## Dataset Creation
+
+### Curation Rationale
+
+<!-- Motivation for the creation of this dataset. -->
+
+[More Information Needed]
+
+### Source Data
+
+<!-- This section describes the source data (e.g. news text and headlines, social media posts, translated sentences, ...). -->
+
+#### Data Collection and Processing
+
+<!-- This section describes the data collection and processing process such as data selection criteria, filtering and normalization methods, tools and libraries used, etc. -->
+
+[More Information Needed]
+
+#### Who are the source data producers?
+
+<!-- This section describes the people or systems who originally created the data. It should also include self-reported demographic or identity information for the source data creators if this information is available. -->
+
+[More Information Needed]
+
+### Annotations
+
+I don't think we did any annotations for parsing only for loading (double check)
+
+#### Personal and Sensitive Information
+
+To our knowledge, this dataset does not contain any private information.
+
+## Bias, Risks, and Limitations
+
+In general, the dataset is highly imbalanced in terms of how many and what protein sequences in Swiss-Prot have an annotation for a given annotation type. This dataset is sparse
+
+
+## Citation [optional]
+
+<!-- If there is a paper or blog post introducing the dataset, the APA and Bibtex information for that should go in this section. -->
+
+**BibTeX:**
+
+[More Information Needed]
+
+
+## Glossary [optional]
+
+<!-- If relevant, include terms and calculations in this section that can help readers understand the dataset or dataset card. -->
+
+[More Information Needed]
+
+## More Information [optional]
+
+[More Information Needed]
+
+## Dataset Card Authors [optional]
+
+[More Information Needed]
+
+## Dataset Card Contact
+
+For any issues with this dataset, please contact martaskreta@cs.toronto.edu or