New data source: PathBank

[gaurav]

Requested by @bazarkua

Request to add: (choose multiple)

• Identifier system
• Mapping source

Urgency: High
Data source name: PathBank
Data source URL: https://pathbank.org/downloads?
Licensing information/URL: ???
Biolink Type of these identifiers: biolink:Pathway, biolink:BiologicalProcess or biolink:MolecularActivity, and biolink:ChemicalEntity
Value of including this source: Needed by NCATSTranslator/translator-ingests#260 (comment), might be a replacement for the not-recently-mapped PathWhiz (#254).

Are there existing identifier sources/mappings in Babel that these identifiers/mappings may conflict
with?

• Yes, we already have 53K pathways (GO, PANTHER.PATHWAY, REACT, SMPDB), 65K biological processes (GO, REACT, UMLS) and 208K molecular activity (TCDB, UMLS, GO, RHEA, EC, KEGG.REACTION, REACT) -- not sure where these will go, but regardless some xrefs to existing identifiers will be necessary.

Any information that will be helpful with working with these identifiers or mappings, including
pointers to existing code for extracting them:

• ???

Next steps:

• Wait for PathBank.org to start working again
• Add PathBank.Reaction and PathBank.Compound as prefixes to the Biolink Model and assign them to the right classes: biolink:Pathway, biolink:BiologicalProcessbiolink:MolecularActivity, and biolink:ChemicalEntity respectively.
• Ingest identifiers
• Figure out cross-references that will allow these reactions to combine with existing ones