Add instruction tuning datasets (#3)

- Add instruction tuning datasets (57b4748c43981b06bb257a71cc316f491e072d53)

.gitattributes

@@ -56,3 +56,6 @@ 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
+integrated_data/v1/protein/protein_func_sim_go_filtered_jaccard.csv filter=lfs diff=lfs merge=lfs -text
+integrated_data/v1/protein/protein_sequences.fa filter=lfs diff=lfs merge=lfs -text
+integrated_data/v1/protein_go/sample_aware_ontology_go_centric/protein_go_relations.unified.csv filter=lfs diff=lfs merge=lfs -text

integrated_data/v1/disgenet/README.md

@@ -0,0 +1,16 @@
+`disgenet_info_filtered.pkl` is a pickled pandas DataFrame containing disease descriptions sourced from:
+ - UMLS
+ - OrphaNet (via PrimeKG)
+ - MONDO (via PrimeKG)
+
+Columns are:
+ - index - unique identifier for this disease / UMLS concept ID in the txPLM datasets
+ - disgenet_id - UMLS ID
+ - various columns named by the sources of the description
+ - allDescriptions - concatenation of all descriptions in the other columns
+ - numDescriptions - total number of unique free text descriptions for this concept ID
+
+Descriptions are concatenated with the `|` symbol, both within one source in the case of multiple
+descriptions from one source, or across all sources in the `allDescriptions` column.
+
+For more details, see the notebook at `../disgenet_curation.ipynb`.

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integrated_data/v1/protein_disgenet/README.md

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+The files in this directory contain gene-disease associations sourced from
+DisGeNET and ClinGen, for more details see the notebook at `../disgenet_curation.ipynb`
+
+`protein_disgenet_relations.csv` contains these associations in a human-readable
+format where `seq_id` corresponds to UniProt IDs and `text_id` corresponds to 
+UMLS concept IDs. 
+
+`protein_disgenet_relations_indexed.csv` contains the same associatons, but with
+`seq_id` now being unique numeric indices to proteins as defined in 
+`../protein/protein_info_filtered.pkl` and `text_id` is the unique numeric index
+to UMLS concept IDs as defined in `../disgenet/disgenet_info_filtered.pkl`.