Add a local API instead of relying on Ensembl

[kimrutherford]

We'll need to think about what to provide. We probably want to keep it minimal but useful because creating our own API is somewhat re-inventing the wheel.

In the meantime I'll have a look at the Ensembl API and MOD/Alliance APIs and make a list of ideas.

It's possible that we'll be able to move over to the Alliance API once the pombe data is integrated. That's a long term plan of course.

See also:

• Review Ensembl Genomes API information #2431

---

Edit:

• https://rest.ensembl.org/
  • https://rest.ensembl.org/homology/id/schizosaccharomyces_pombe/SPBC460.01c?content-type=application/json
• https://www.alliancegenome.org/swagger-ui/

[kimrutherford]

I've started a wiki page with API ideas:

• https://github.com/pombase/website/wiki/APIPlanning

[ValWood]

Great start. This might be sufficient. We can always add more as asked...

[kimrutherford]

Let's have a chat about that list sometime. I'm not sure any of my suggestions are very useful. A mapping tool and perhaps gene details are they only things I would possibly use if I had to work with pombe data.

For everything else (especially annotation) the download files are easier to work with.

[PCarme]

For everything else (especially annotation) the download files are easier to work with.

I have definitely been asked if there was a way to download all annotations to a set of terms in the past, so at least that would be useful to some people

[kimrutherford]

I have definitely been asked if there was a way to download all annotations to a set of terms in the past, so at least that would be useful to some people

I guess they would want the annotation for the descendant terms included in the download?

If we provide that function we should add a "Download all annotation" button on each term page as a shortcut.
https://www.pombase.org/term/GO:0000070

[ValWood]

If we provide that function we should add a "Download all annotation" button on each term page as a shortcut.
https://www.pombase.org/term/GO:0000070

This wouldnt hewld for a set of terms though.

People quite often ask for "all annotations to a gene " for all genes (i.e., including ancestors), but this usually indicates that the tools/ code they are using is not ontology aware...

[PCarme]

I guess they would want the annotation for the descendant terms included in the download?

I would assume yes.

If we provide that function we should add a "Download all annotation" button on each term page as a shortcut.

That would make it simple to find when browsing the website.

[kimrutherford]

I've implemented the easiest API first: a gene lookup.

It works by passing a comma separated list of systematic IDs:
https://www.pombase.org/rest/genes/by_id/SPBC216.07c,SPBC18H10.20c

On the command line it can be accessed with "curl":

curl https://www.pombase.org/rest/genes/by_id/SPBC216.07c > results.json

The JSON result contains most of the gene details, except for annotation. The URL and return format will need fine-tuning.

Below is a sample of the sort of details that are returned, with a few things skipped for brevity. I forgot to add a "transcripts" field with the transcript and protein details. I'll do that next.

[
  {
    "systematic_id": "SPBC216.07c",
    "name": "tor2",
    "taxonid": 4896,
    "product": "TORC1 serine/threonine protein kinase Tor2",
    "deletion_viability": "inviable",
    "uniprot_identifier": "Q9Y7K2",
    "biogrid_interactor_id": 277243,
    "interpro_matches": [
      {
        "id": "PF02260",
        "dbname": "PFAM",
        "name": "FATC",
        "description": "FATC domain",
        "interpro_id": "IPR003152",
        "interpro_name": "FATC_dom",
        "interpro_description": "FATC domain",
        "match_start": 2307,
        "match_end": 2337,
        "locations": [
          {
            "start": 2307,
            "end": 2337
          }
        ]
      },
      ...
    ],
    "low_complexity_region_coords": [ ... ],
    "coiled_coil_coords": [
      {
        "range": {
          "start": 1296,
          "end": 1316
        }
      }
    ],
    "chains": [
      {
        "range": {
          "start": 1,
          "end": 2337
        },
        "assigned_by": "UniProtKB"
      }
    ],
    "orfeome_identifier": "34/34C09",
    "schizosaccharomyces_orthogroup": "SOG_2082",
    "pombephosphoproteomics_unige_ch_starvation_mating_gene": "Q9Y7K2",
    "synonyms": [
      {
        "name": "SPBC646.01c",
        "type": "exact"
      }
    ],
    "dbxrefs": [
      "SPD:34/34C09"
    ],
    "feature_type": "mRNA gene",
    "feature_so_termid": "SO:0000704",
    "transcript_so_termid": "SO:0000234",
    "characterisation_status": "biological role published",
    "taxonomic_distribution": "eukaryotes only, fungi and metazoa",
    "location": {
      "chromosome_name": "chromosome_2",
      "start_pos": 915085,
      "end_pos": 922352,
      "strand": "reverse"
    },
    "gocams": [
      {
        "gocam_id": "6796b94c00006848",
        "title": "TORC1 signaling (GO:0038202)"
      }
    ]
  },
  {
      "systematic_id": "SPBC18H10.20c",
      ..., 
  }
]