Accessive API

This documentation covers the usage of the Accessive API for mapping biological identifiers.

API Endpoint

/map - Map a list of identifiers from one type to another.

HTTP Methods

GET, POST

Parameters

Name	Description	Required
ids	A list of identifiers to map.	Yes
from_type	The type of the identifiers to map.	Yes
to_types	A list of types to map the identifiers to.	Yes
taxon	The taxon to map the identifiers in. (NB: Human is 9606.)	Yes
format	The format to return the results in. Options: 'txt', 'json'. Default is 'json'.	No

Response

The API returns a JSON object containing the mapping results or an error message.

Example Requests

Below are examples demonstrating how to make a request to the /map endpoint using curl and the Python requests library.

Using curl

curl -X GET "https://alexander.bio/accessive/api/map?ids=ENSG00000139618&from_type=ensembl_gene&to_types=uniprot_swissprot&taxon=9606"

Using Python requests

import requests

url = "https://alexander.bio/accessive/api/map"
params = {
    "ids": "ENSG00000139618",
    "from_type": "ensembl_gene",
    "to_types": "uniprot_swissprot",
    "taxon": "9606"
}
response = requests.get(url, params=params)
print(response.json())

Available Identifier Types

Gene level:

ensembl_gene: Ensembl Gene (Ensembl gene identifier)
gene_description: Short plaintext description of the gene
gene_name: Gene Name (Name of the gene)
arrayexpress: ArrayExpress (Microarray data repository)
biogrid: BioGRID (Biological interaction database)
ens_lrg_gene: ENS_LRG_gene (Locus Reference Genomic gene ID)
entrez_gene: EntrezGene (NCBI gene identifier)
genecards: GeneCards (Human gene compendium)
hgnc: HGNC (HUGO Gene Nomenclature Committee ID)
mim_gene: MIM_GENE (Mendelian Inheritance in Man gene ID)
pfam: Pfam (Protein family database)
uniprot_gene: Uniprot_gn (UniProt gene name)
wikigene: WikiGene (Collaborative gene wiki)
nextprot: neXtProt (Human protein database)

Transcript level:

ensembl_mrna: Ensembl mRNA (Ensembl mRNA identifier)
ccds: CCDS (Consensus CDS project ID)
ens_lrg_transcript: ENS_LRG_transcript (LRG transcript identifier)
refseq_mrna: RefSeq mRNA (NCBI mRNA reference sequence)
refseq_ncrna: RefSeq ncRNA (NCBI non-coding RNA reference)
ucsc: UCSC (UCSC Genome Browser ID)
isoform_biotype: Isoform Biotype (Gene isoform biotype classification)

Protein level:

ensembl_prot: Ensembl Protein (Ensembl protein identifier)
uniparc: UniParc (UniProt Archive identifier)
alphafold: AlphaFold (Protein structure prediction database)
uniprot_swissprot: Uniprot/SWISSPROT (UniProtKB/Swiss-Prot ID)
uniprot_trembl: Uniprot/SPTREMBL (UniProtKB/TrEMBL ID)
uniprot_isoform: Uniprot Isoform (UniProt isoform identifier)
refseq_peptide: RefSeq Peptide (NCBI peptide reference sequence)
embl: EMBL (European Molecular Biology Lab sequence ID)
pdb: PDB (Protein Data Bank identifier)