add record for iPTMnet API

[andrewsu]

Data Source

Optional. Name of the preferred source for this data. E.g. OMIM, DrugBank

• iPTMnet -- more info at https://research.bioinformatics.udel.edu/iptmnet/

Main Entity Type

What kind of entity are you interested in? Biolink type preferred, e.g. variant, disease, gene

• SUBJECT: Protein

Connected Entity Type

What kind of thing should the subject be connected to? E.g. for drug-disease links this would be 'disease'. Biolink type preferred

• OBJECT: Protein

• RELATION: entity regulated by entity / entity regulates entity

Example statement

Enter one or more examples of statements/edges you would expect to retrieve using this source. For example, "aldehydes exacerbates Fanconi anemia". In future this could be used to drive integration tests

• EXAMPLE 1: CDK2 is phosphorylated by CDK7

From https://research.bioinformatics.udel.edu/iptmnet/api/P24941/substrate, this snippet asserts that CDK7 phosphorylates CDK2 with various bits of provenance

{
  "residue": "T",
  "site": "T165",
  "ptm_type": "Phosphorylation",
  "score": 3,
  "sources": [
    {
      "name": "RLIMS-P",
      "label": "rlimsp",
      "url": "http://research.bioinformatics.udel.edu/rlimsp/"
    },
    {
      "name": "PSP",
      "label": "psp",
      "url": "http://www.phosphosite.org/"
    }
  ],
  "enzymes": [
    {
      "id": "P50613",
      "enz_type": "uniprot_ac",
      "name": "CDK7"
    }
  ],
  "pmids": [
    "18396144"
  ]
}

• EXAMPLE 2: CDK2 phosphorylates MCM4

From https://research.bioinformatics.udel.edu/iptmnet/api/P24941/as-enzyme, this snippet asserts that CDK2 phosphorylates MCM4 with various bits of provenance

{
  "substrate": "P33991",
  "substrate_symbol": "MCM4",
  "site": "S3",
  "score": 0,
  "sources": [
    {
      "name": "HPRD",
      "label": "hprd",
      "url": "http://www.hprd.org/"
    }
  ],
  "pmids": [
    "19651622",
    "16519687",
    "20068231"
  ]
}

Preferred format or ingest method

How would you prefer to get the data? Via API or Data dump that can be ingested into your KG? Would you prefer a smart API registry entry, a neo4j dump, biolink-compliant CSV/RDF/JSON that can be loaded with KGX?

• METHOD: SmartAPI annotation -- note existing Swagger documentation at https://research.bioinformatics.udel.edu/iptmnet/api/doc/

[colleenXu]

I've written a SmartAPI yaml w/ x-bte annotation for this resource based on the resource's swagger v2 doc (page, source json). It covers the two endpoints / situations Andrew described above.

However, this isn't ready yet:

• I wasn't able to test this yaml or look at the /as-enzyme response as I was writing because the resource was down this evening (both swagger v2 doc page and resource website). It didn't seem to be down yesterday...
• I'm not sure if the current response-mapping / post-processing will work.
  • I think the API response is a json object where the keys are the matching proteoform IDs (ex: P24941, P24941-1, P24941-2) and the values are the arrays of PTM info that have the protein ID/pmids that we want.
  • so the top-level keys aren't static and I'm not sure if we need custom post-processing to handle this and get the deeper-level info we want...

Notes:

• I only annotated the endpoints we wanted to use
• I did a quick try of the other endpoints: some queries failed and others had responses but I didn't notice anything that'd be easy to annotate for Translator (associations between bioentities with IDs)

[colleenXu]

Related infores stuff is ready but not deployed yet:

• new infores catalog entry for iPTMnet in PR https://github.com/biolink/biolink-model/pull/1429
• made new infores pages for iPTMnet (primary knowledge source)

[colleenXu]

Small update

while the api page (swagger v2) and website are back up as of Monday, the GET requests are still failing tonight:

• for the example substrate query above, I'm getting a 500 (internal server error) with the response IO error: No route to host (os error 113)
• for the example as-enzyme query above, I'm getting a 404 (Not Found)

So I haven't tested the x-bte annotation yet...

[colleenXu]

Moving to on-hold in https://github.com/orgs/biothings/projects/12/views/1, still waiting for the GET requests to succeed so I can test the x-bte annotation

[colleenXu]

@newgene @andrewsu

I haven't been able to get a successful response from this API since 12/6. I've been occasionally doing the example queries to see if I get a successful response and haven't gotten one.

It may be a good idea to contact that group to ask about their API? They wrote a paper on their API work in 2020, which isn't that long ago https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7216315/

I'm also wondering if standing up a BioThings API for this data is a good idea...

• The license for the database is CC BY-NC-SA 4.0 (Attribution-NonCommercial-ShareAlike 4.0 International) license, according to https://research.bioinformatics.udel.edu/iptmnet/license
• download available at https://research.bioinformatics.udel.edu/iptmnet/download
• seems to be regularly updated (last update yesterday) https://research.bioinformatics.udel.edu/iptmnet/stat

[newgene]

👍 seems a good candidate of building an API out of their data