Geneset annotation data

Data sources

We currently obtain the geneset annotation data from several public data resources and keep them up-to-date, so that you don’t have to do it:

Source	Update frequency
MSigDB	whenever a new release is available
Gene Ontology	whenever a new release is available
KEGG	whenever a new release is available
WikiPathways	whenever a new release is available
Reactome	whenever a new release is available
Disease Ontology	whenever a new release is available

The most updated data information can be accessed here.

Geneset object

Geneset annotation data are both stored and returned as a geneset object, which is essentially a collection of fields (attributes) and their values:

{
  "_id": "WP60",
  "_version": 1,
  "genes": [
    {
      "ensemblgene": "YOL165C",
      "mygene_id": "853999",
      "name": "putative aryl-alcohol dehydrogenase",
      "ncbigene": "853999",
      "symbol": "AAD15",
      "uniprot": "Q08361"
    },
    {
      "mygene_id": "850488",
      "name": "pseudo",
      "ncbigene": "850488",
      "symbol": "AAD6"
    },
    {
      "ensemblgene": "YNL331C",
      "mygene_id": "855385",
      "name": "putative aryl-alcohol dehydrogenase",
      "ncbigene": "855385",
      "symbol": "AAD14",
      "uniprot": "P42884"
    },
    {
      "ensemblgene": "YCR107W",
      "mygene_id": "850471",
      "name": "putative aryl-alcohol dehydrogenase",
      "ncbigene": "850471",
      "symbol": "AAD3",
      "uniprot": "P25612"
    },
    {
      "ensemblgene": "YJR155W",
      "mygene_id": "853620",
      "name": "putative aryl-alcohol dehydrogenase",
      "ncbigene": "853620",
      "symbol": "AAD10",
      "uniprot": "P47182"
    },
    {
      "ensemblgene": "YDL243C",
      "mygene_id": "851354",
      "name": "putative aryl-alcohol dehydrogenase",
      "ncbigene": "851354",
      "symbol": "AAD4",
      "uniprot": "Q07747"
    }
  ],
  "is_public": true,
  "name": "Toluene degradation",
  "source": "wikipathways",
  "taxid": 559292,
}

The example above contains the most common available fields, but omits some fields that are specific to specific data sources. For a full example, you can check out a few examples: GO_0004568_9606 (a Gene Ontology geneset), WP60 (a Wikipathways geneset), or find a list of the available fields at: http://mygeneset.info/v1/metadata/fields

_id field

Each individual geneset object contains an “_id” field as the primary key. The value of the “_id” field is different for every built-in data source, but is typically the primary ID used in the source data. For example, for MSigDB, this is the original geneset id. For genesets coming from metabolic pathway databases (KEGG, GO, Wikipathways) which contain multiple species, _id is typically a combination of the pathway id, plus the organism taxid. User-submitted genesets have randomly generated _id fields. Here is an example. If searching for a particular GO term, or KEGG ID using the query endpoint, we recommend using “kegg.id”or “go.id”, plus the species filter instead of “_id”.

Note

Regardless how the value of the “_id” field looks like, it always works for our geneset annotation service /v1/geneset/<geneid>.

_score field

You will often see a “_score” field in the returned geneset object, which is the internal score representing how well the query matches the returned geneset object. It probably does not mean much in the geneset annotation service when only one geneset object is returned. In the geneset query service, by default, the returned geneset hits are sorted by the scores in descending order.

Species filter

We support ALL species annotated by NCBI and Ensembl. All of our services allow you to pass a “species” parameter to limit the query results. “species” parameter accepts taxonomy ids as the input. You can look for the taxomony ids for your favorite species from NCBI Taxonomy.

For convenience, we allow you to pass these common names for commonly used species (e.g. “species=human,mouse,rat”):

Search term (common name)	Genus name	Taxonomy id
human	Homo sapiens	9606
mouse	Mus musculus	10090
rat	Rattus norvegicus	10116
mosquito	Anopheles gambiae	180454
fruitfly	Drosophila melanogaster	7227
nematode	Caenorhabditis elegans	6239
zebrafish	Danio rerio	7955
thale-cress	Arabidopsis thaliana	3702
rice	Oryza sativa	39947
dog	Canis lupus familiaris	9615
chicken	Gallus gallus	9031
horse	Equus caballus	9796
chimpanzee	Pan troglodytes	9598
frog	Xenopus tropicalis	8364
pig	Sus scrofa	9823
pseudomonas-aeruginosa	Pseudomonas aeruginosa	208964
brewers-yeast	Saccharomyces cerevisiae	559292

If needed, you can pass “species=all” to query against all available species, although, we recommend you to pass specific species you need for faster response.