Nichollette Acosta

Working example of the association structure for metabolite HMDB data below... For an example of the data file and one protein, see [here](https://github.com/NikkiBytes/BioThings_dojo/blob/main/data_plugins/hmdb_proteins/proteins.xml). This is what I am currently extracting...

Example of the newly edited structure, was able to pull the `protein_type`, and added the alternative IDs. Integrating into an API now. ``` [ { "_id": "HMDBP00001_1", "pmid": "11752352", "subject":...

Here is an example output of a single record generated with the parser.... ``` { "_id": "HMDBP00001_1", "pmid": "11752352", "subject": { "protein_type": "Unknown", "uniprot_id": "P21589", "uniprot_name": "5NTD_HUMAN", "genbank_protein_id": "23897", "hgnc_id":...

Thank you @zcqian , the logs .... ``` root | OPTIONS args: ('prot_meta_assc_hmdb.prot_meta_assc_hmdb',), kwargs: {} | 2021-10-13T20:39:00 -- | -- | -- tornado.access | 200 OPTIONS /source/prot_meta_assc_hmdb.prot_meta_assc_hmdb/upload (172.17.0.1) 1.48ms |...

A few notes/updates on the parser..... - Fixed ERROR `BAD CRC-32`: The input metabolite file, `hmdb_metabolites.xml` from [HMDB downloads](https://hmdb.ca/downloads), the files current version 5.0 is corrupt and produces the error....

The parser and manifest repo is [here](https://github.com/NikkiBytes/orthologyAGR) . A few tests queries can be found in [this notebook](https://github.com/NikkiBytes/BioThings_dojo/blob/main/data_plugins/orthoAGR/notebooks/Ortho-AGR_Plugin_Testing.ipynb). The repo was passed along for final deployment into mygene API, will...

@zcqian it's added!

A few updates.... The document structure has been updated, example output below: ``` [ { "_id": "176377", "agr": { "ortholog": [ { "geneid": "SGD:S000003566", "symbol": "VPS53", "taxid": "NCBITaxon:559292", "algorithmsmatch": 9,...