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bioData: Web Services: REST Web Services

Documentation using bioData through REST web services

Get a list of avaliable databases
Get a list of tables for a database
Get information about a table
Query a table

Get a list of avaliable databases

http://biodata.abcc.ncifcrf.gov/rest/v1/databases

{
    "AFFY": {
        "long_name": "Affymetrix"
    },
    "AGILENT": {
        "long_name": "AGILENT"
    },
    "BIOCARTA": {
        "long_name": "Biocarta"
    },
    "BIOGRID": {
        "long_name": "Biological General Repository for Interaction Datasets (BioGRID)"
    },
    "BLOCKS": {
        "long_name": "BLOCKS"
    },
    "CCDS": {
        "long_name": "The Consensus CDS (CCDS)"
    },
    "CGAP": {
        "long_name": "Cancer Genome Anatomy Project (CGAP)"
    },
    "CTD": {
        "long_name": "Comparative Toxicogenomics Database (CTD)"
    },
    "DBSNP": {
        "long_name": "dbSNP"
    },
    "DBVAR": {
        "long_name": "dbVar"
    },
    "DIP": {
        "long_name": "Database of Interacting Proteins (DIP)"
    },
    "DRUGBANK": {
        "long_name": "DrugBank"
    },
    "ENSEMBL": {
        "long_name": "Ensembl"
    },
    "GAD": {
        "long_name": "Genetic Association Database (GAD)"
    },
    "GBK": {
        "long_name": "GenBank"
    },
    "GENE": {
        "long_name": "EntrezGene"
    },
    "GENE3D": {
        "long_name": "GENE3D"
    },
    "GENETESTS": {
        "long_name": "GeneTests"
    },
    "GNF": {
        "long_name": "Genomics Institute of the Novartis Research Foundation (GNF)"
    },
    "GO": {
        "long_name": "Gene Ontology (GO)"
    },
    "GPT": {
        "long_name": "GenPept"
    },
    "GSEA": {
        "long_name": "Gene Set Enrichment Analysis (GSEA)"
    },
    "GWASDB": {
        "long_name": "GWASdb"
    },
    "HINV": {
        "long_name": "H-Invitational (H-Inv)"
    },
    "HMDB": {
        "long_name": "Human Metabolome Database (HMDB)"
    },
    "HMDD": {
        "long_name": "Human MicroRNA Disease Database (HMDD)"
    },
    "HOMOLOGENE": {
        "long_name": "HomoloGene"
    },
    "HPRD": {
        "long_name": "Human Protein Reference Database (HPRD)"
    },
    "INTACT": {
        "long_name": "IntAct - open source resource for molecular interaction data"
    },
    "INTERPRO": {
        "long_name": "InterPro"
    },
    "KEGG": {
        "long_name": "Kyoto Encyclopedia of Genes and Genomes (KEGG)"
    },
    "MGC": {
        "long_name": "Mammalian Gene Collection (MGC)"
    },
    "MINT": {
        "long_name": "The Molecular INTeraction database (MINT)"
    },
    "MIR2DISEASE": {
        "long_name": "miR2Disease"
    },
    "MIRTARBASE": {
        "long_name": "miRTarBase"
    },
    "NCIPID": {
        "long_name": "NCI-Pathway Interaction Database (NCI-PID)"
    },
    "OMIM": {
        "long_name": "Online Mendelian Inheritance in Man (OMM)"
    },
    "PFAM": {
        "long_name": "Pfam"
    },
    "PHARMGKB": {
        "long_name": "Pharmacogenomics Knowledge Base (PharmGKB)"
    },
    "PIRSF": {
        "long_name": "Protein Information Resource SuperFamily (PIRSF)"
    },
    "PRINTS": {
        "long_name": "PRINTS"
    },
    "PRODOM": {
        "long_name": "ProDom"
    },
    "PSI_MI": {
        "long_name": "Proteomics Standards Initiative - Molecular Interactions (PSI-MI)"
    },
    "REACTOME": {
        "long_name": "REACTOME"
    },
    "REFN": {
        "long_name": "RefSeq Nucleotide"
    },
    "REFP": {
        "long_name": "RefSeq Protein"
    },
    "SAFARI": {
        "long_name": "Kinase SARfari"
    },
    "STITCH": {
        "long_name": "STITCH: interaction networks of chemicals and proteins"
    },
    "STRING": {
        "long_name": "String"
    },
    "SUPFAM": {
        "long_name": "SUPERFAMILY"
    },
    "TAXON": {
        "long_name": "Taxonomy"
    },
    "TCAG": {
        "long_name": "Database of Genomic Variants (DGV)"
    },
    "TGI": {
        "long_name": "Resourcerer"
    },
    "TRANSFAC": {
        "long_name": "TRANFAC"
    },
    "UNIGENE": {
        "long_name": "UniGene"
    },
    "UNIPROT": {
        "long_name": "Universal Protein Resource (UniProt)"
    },
    "UNISTS": {
        "long_name": "UniSTS"
    },
    "WGS": {
        "long_name": "Whole-Genome Shotgun (WGS)"
    }
}



Get a list of tables for a database

http://biodata.abcc.ncifcrf.gov/rest/v1/databases/<DATABASE>

<DATABASE> = one of the database name, for example, "gene"

Example: http://biodata.abcc.ncifcrf.gov/rest/v1/databases/gene

{
    "tables": [
        "GENE2ACCESSION",
        "GENE2GO",
        "GENE2PUBMED",
        "GENE2REFSEQ",
        "GENE2STS",
        "GENE2UNIGENE",
        "GENEHISTORY",
        "GENERIFS_BASIC",
        "GENE_DBXREF",
        "GENE_INFO",
        "GENE_SYN",
        "HOMOLOGENE",
        "INTERACTIONS",
        "MIM2GENE",
        "REFP2UNIPROT",
        "SUMMARY_HS"
    ]
}


Get information about a table

http://biodata.abcc.ncifcrf.gov/rest/v1/databases/<DATABASE>/<TABLE>

<DATABASE> = one of the database name, for example, "gene"

<TABLE> = one of the table name from the database, for example, "gene2go"

Example: http://biodata.abcc.ncifcrf.gov/rest/v1/databases/gene/gene2go

{
    "TAXID": {
        "data_type": "NUMBER(22)",
        "column_description": "the unique identifier provided by NCBI Taxonomy for the species or strain/isolate"
    },
    "GENEID": {
        "data_type": "VARCHAR2(15)",
        "column_description": "the unique identifier for a gene"
    },
    "GOID": {
        "data_type": "VARCHAR2(20)",
        "column_description": "the GO ID, formatted as GO:0000000"
    },
    "EVIDENCE": {
        "data_type": "VARCHAR2(50)",
        "column_description": "the evidence code in the gene_association file"
    },
    "GOQUALIFIER": {
        "data_type": "VARCHAR2(100)",
        "column_description": "a qualifier for the relationship between the gene and the GO term"
    },
    "GODESCRIPTION": {
        "data_type": "VARCHAR2(255)",
        "column_description": "the term indicated by the GO ID"
    },
    "PUBMEDIDS": {
        "data_type": "VARCHAR2(250)",
        "column_description": "pipe-delimited set of PubMed uids reported as evidence for the association"
    },
    "CATEGORY": {
        "data_type": "VARCHAR2(9)",
        "column_description": "the GO category (Function, Process, or Component)"
    }
}


Query a table

http://biodata.abcc.ncifcrf.gov/rest/v1/databases/<DATABASE>/<COLUMN>/<QUERY STRING>

This API will return result that contains the QUERY STRING (*QUERY STRING*)

<DATABASE> = one of the database name

<TABLE> = one of the table name from the database

<COLUMN> = name of one column from the table

<QUERY STRING> = query string 

Example: http://biodata.abcc.ncifcrf.gov/rest/v1/databases/agilent/agilent_metadata/chip_type/microarray


[
    {
        "PLATFORM_ID": "Agilent-023795",
        "CHIP_TYPE": "dna_meth_microarray",
        "METADATA_TITLE": "description",
        "METADATA": " Human DNA Methylation Microarray 244k Arrays of this design have barcodes that begin with 16023795 or 2523795. Orientation: Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software. The ID column represents the Agilent Feature Extraction feature number. Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface). To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions."
    },
    {
        "PLATFORM_ID": "Agilent-023795",
        "CHIP_TYPE": "dna_meth_microarray",
        "METADATA_TITLE": "distribution",
        "METADATA": " commercial"
    },
    {
        "PLATFORM_ID": "Agilent-023795",
        "CHIP_TYPE": "dna_meth_microarray",
        "METADATA_TITLE": "manufacture_protocol",
        "METADATA": " see manufacturer's web site at http://www.agilent.com/"
    },
    {
        "PLATFORM_ID": "Agilent-023795",
        "CHIP_TYPE": "dna_meth_microarray",
        "METADATA_TITLE": "manufacturer",
        "METADATA": " Agilent Technologies"
    },
    {
        "PLATFORM_ID": "Agilent-023795",
        "CHIP_TYPE": "dna_meth_microarray",
        "METADATA_TITLE": "organism",
        "METADATA": " Homo sapiens"
    },
    {
        "PLATFORM_ID": "Agilent-023795",
        "CHIP_TYPE": "dna_meth_microarray",
        "METADATA_TITLE": "technology",
        "METADATA": " in situ oligonucleotide"
    },
    {
        "PLATFORM_ID": "Agilent-023795",
        "CHIP_TYPE": "dna_meth_microarray",
        "METADATA_TITLE": "title",
        "METADATA": " Agilent-023795 Human DNA Methylation Microarray 244k "
    }
]