Plugin ebi_data_parser renaming and update

[erikyao]

Renaming

• Old: https://github.com/erikyao/ebi_data_parser
• New: https://github.com/erikyao/ebi_gene2phenotype

Update

Data files updated to 24_6_2023 version. Last deployment used 19_2_2020.

Mapping also changed.

[erikyao]

Related: #43

[andrewsu]

@erikyao just to check, did the API document structure change in the latest version update? If yes, we may need to review/revise the SmartAPI annotation...

[erikyao]

@andrewsu, yes, it has changed due to the updated data files. I can paste the old vs. new mapping below ASAP.

[erikyao]

Old

New

{ "mapping": { "gene2phenotype": { "properties": { "gene_symbol": { "normalizer": "keyword_lowercase_normalizer", "type": "keyword" }, "gene_mim": { "normalizer": "keyword_lowercase_normalizer", "type": "keyword" }, "disease": { "properties": { "disease_name": { "type": "text" }, "disease_mim": { "normalizer": "keyword_lowercase_normalizer", "type": "keyword" } } }, "organ_specificity_list": { "type": "text" }, "pmids": { "type": "integer" }, "panel": { "normalizer": "keyword_lowercase_normalizer", "type": "keyword" }, "gene_disease_pair_entry_date": { "normalizer": "keyword_lowercase_normalizer", "type": "keyword" }, "prev_symbols": { "normalizer": "keyword_lowercase_normalizer", "type": "keyword" }, "phenotypes": { "normalizer": "keyword_lowercase_normalizer", "type": "keyword" }, "allelic_requirement": { "type": "text" }, "DDD_category": { "type": "text" }, "mutation_consequence": { "type": "text" } } } } }

{ "mapping": { "gene2phenotype": { "properties": { "gene_symbol": { "normalizer": "keyword_lowercase_normalizer", "type": "keyword" }, "gene_mim": { "normalizer": "keyword_lowercase_normalizer", "type": "keyword" }, "disease": { "properties": { "disease_name": { "type": "text" }, "disease_mim": { "normalizer": "keyword_lowercase_normalizer", "type": "keyword" } } }, "confidence_category": { "normalizer": "keyword_lowercase_normalizer", "type": "keyword" }, "allelic_requirement": { "normalizer": "keyword_lowercase_normalizer", "type": "keyword" }, "organ_specificity_list": { "type": "text" }, "pmids": { "type": "integer" }, "panel": { "normalizer": "keyword_lowercase_normalizer", "type": "keyword" }, "gene_disease_pair_entry_date": { "normalizer": "keyword_lowercase_normalizer", "type": "keyword" }, "variant_consequence": { "normalizer": "keyword_lowercase_normalizer", "type": "keyword" }, "prev_symbols": { "normalizer": "keyword_lowercase_normalizer", "type": "keyword" }, "phenotypes": { "normalizer": "keyword_lowercase_normalizer", "type": "keyword" }, "disease_ontology": { "normalizer": "keyword_lowercase_normalizer", "type": "keyword" }, "confidence_value_flag": { "type": "text" }, "mutation_consequence_flag": { "type": "text" }, "mutation_consequence": { "type": "text" }, "cross_cutting_modifier": { "type": "text" } } } } }

[erikyao]

@andrewsu @colleenXu I have pasted the old vs new mapping in the above comment

[colleenXu]

After a shallow review of the new/existing fields, I made a basic update to the SmartAPI yaml and x-bte annotation here NCATS-Tangerine/translator-api-registry@62fd322

Most of this effort will be commented out for now in another commit, due to biothings/biothings_explorer#587 (comment)

This issue can be closed, since this parser update has been completed for now.