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Biothings API

Overview

BioThings.io is a collection of APIs that provide comprehensive data annotation services for various types of biomedical information. It is designed to facilitate data access and integration for researchers working in genomics, drug discovery, and related fields. BioThings APIs are optimized for high-speed queries and data annotation, making it an essential tool for accessing gene, variant, chemical, and disease-related information.

Key BioThings APIs

BioThings offers four main services, each specializing in a specific type of annotation:

  1. MyGene.info: Provides gene-centric annotation, including gene descriptions, biological functions, interactions, and pathway information.
  2. MyVariant.info: Focuses on variant annotation, offering detailed insights into genetic variations, their impacts, and clinical significance.
  3. MyChem.info: A chemical and drug annotation service that provides data on chemical structures, drug interactions, and pharmacological information.
  4. MyDisease.info: Specializes in disease annotation, linking diseases to associated genes, phenotypes, clinical trials, and more.

Each of these services is designed to be scalable, fast, and accessible via a simple RESTful API interface.

Services Overview

1. MyGene.info

  • Description: MyGene.info offers a powerful gene annotation service, providing researchers access to comprehensive gene-centric data. It aggregates information from various sources such as NCBI, Ensembl, UniProt, and more.
  • Key Features:
    • Gene descriptions and summaries
    • Biological functions and interactions
    • Pathway information
    • Support for human and model organism genes

2. MyVariant.info

  • Description: MyVariant.info is a variant-centric service that delivers high-quality annotations for genetic variations. It aggregates variant data from multiple sources, including dbSNP, ClinVar, and ExAC.
  • Key Features:
    • Population frequencies
    • Clinical significance and pathogenicity
    • Functional predictions and annotations
    • Support for SNPs, indels, and structural variants

3. MyChem.info

  • Description: MyChem.info provides an efficient way to retrieve chemical and drug annotations. It integrates data from ChEMBL, DrugBank, PubChem, and other chemical databases.
  • Key Features:
    • Chemical structure and formula
    • Drug interactions and adverse effects
    • Pharmacological properties and indications
    • Toxicology and safety information

4. MyDisease.info

  • Description: MyDisease.info is a disease-centric annotation service designed to provide detailed information about human diseases, including gene-disease associations, clinical trials, and ontology information.
  • Key Features:
    • Disease descriptions and ontology terms
    • Gene and variant associations
    • Links to clinical trials and disease models
    • Disease-gene interaction networks

How to Access

Each of the BioThings APIs provides a well-documented RESTful interface, allowing users to send simple HTTP queries to retrieve data in JSON format. The APIs support a wide range of query options, including gene/variant/disease names, chemical identifiers, and specific properties.

Biothing's API (https://biothings.io/)

MyGene.info (https://mygene.info/)

MyVariant.info (https://myvariant.info/)

MyChem.info (https://mychem.info/)

MyDisease.info (https://mydisease.info/)

Querying Genes

You can query genes from BioThings' MyGene.info API using a variety of identifiers and attributes. Here are the main types of queries you can run:

1. Retrieve Gene Information by Specific ID

  • You can look up detailed gene information using various gene identifiers:
    • Entrez Gene ID: https://mygene.info/v3/gene/1017
    • Ensembl Gene ID: Similar format to Entrez ID queries.
    • UniProt ID: Example query: https://mygene.info/v3/query?q=uniprot:P24941

2. Search by Gene Symbol

  • Retrieve genes by their symbol (e.g., CDK2):
    • https://mygene.info/v3/query?q=symbol:cdk2

3. Search by Gene Summary Text

  • Search for genes based on their descriptions or related summaries. For example, to get genes related to "Insulin":
    • https://mygene.info/v3/query?q=summary:insulin

4. Retrieve Data Source Metadata

  • Retrieve metadata about the sources of gene data:
    • https://mygene.info/metadata

5. Get a List of All Available Fields

  • Get a list of all fields available in the MyGene.info database:
    • https://mygene.info/metadata/fields

These queries provide flexible options for retrieving gene-centric data using different identifiers, symbols, or biological descriptions.

Querying Variants

You can query variants from BioThings' MyVariant.info API using various types of identifiers, genomic coordinates, and annotation criteria. Below is a summary of the main types of queries:

1. Retrieve Variant by Specific HGVS ID

  • Look up variant information using a specific HGVS (Human Genome Variation Society) ID:
    • https://myvariant.info/v1/variant/chr7:g.55241707G>T

2. Retrieve Variants Based on Specific Annotations

  • Query for variants that have specific annotations, such as those annotated in ClinVar:
    • https://myvariant.info/v1/query/?q=_exists_:clinvar

3. Find Variants for a Specific Gene

  • Retrieve all non-synonymous variants for a given gene using its symbol, e.g., BTK:
    • https://myvariant.info/v1/query/?q=dbnsfp.genename:BTK

4. Search Variants by Genomic Range

  • Search for variants within a specified genomic range:
    • https://myvariant.info/v1/query/?q=chr1:69000-70000

5. Complex Queries Combining Multiple Annotations

  • Create advanced queries that combine multiple annotations (e.g., variants with wellderly annotation and possibly damaging CADD PolyPhen predictions):
    • https://myvariant.info/v1/query/?q=_exists_:wellderly AND cadd.polyphen.cat:possibly_damaging&fields=wellderly,cadd.polyphen

6. Retrieve Data Source Metadata

  • Retrieve metadata about the sources of variant data:
    • https://mygene.info/metadata/

7. Get a List of All Available Fields

  • Get a complete list of all fields available in MyVariant.info:
    • https://mygene.info/metadata/fields

These queries enable a comprehensive exploration of variant data using various identifiers, genomic ranges, annotations, and gene symbols.

Example Gene querying results

Here's a categorized table summarizing the useful information from the given JSON file:

Category Field Name Description/Content
Identifiers AllianceGenome 1771
HGNC 1771
MIM 116953
_id 1017
entrezgene 1017
ensembl Gene: ENSG00000123374, Protein: multiple ENSP, Transcript: multiple ENST
symbol CDK2 (Cyclin Dependent Kinase 2)
other_names cdc2-related protein kinase, cell division protein kinase 2, p33 protein kinase
Accession Numbers accession Genomic, Protein, RNA, Translation
protein Various accession numbers: e.g., AAA35667.1, NP_001277159.1
rna Various accession numbers: e.g., NM_001290230.2, XM_011537732.2
Aliases alias CDKN2, p33(CDK2)
Chemical Data chembl Multiple entries linking to ChEMBL data, e.g., CHEMBL4106153
Genomic Position genomic_pos chr 12: 55966781-55972789, Strand: 1
genomic_pos_hg19 chr 12: 56360553-56366568, Strand: 1
Ensembl Information ensembl Gene: ENSG00000123374, multiple protein and transcript identifiers
type_of_gene protein_coding
Functional Annotations go Gene Ontology (GO) annotations for BP, MF, and CC categories
BP Biological processes like G1/S transition, protein phosphorylation, signal transduction
CC Cellular components: nucleus, centrosome, cyclin-CDK complex
MF Molecular functions: ATP binding, cyclin binding, protein kinase activity
Orthologs orthologs Homologous genes across multiple species
Pathway Information pathway Various pathway identifiers: BioCarta, KEGG, NetPath, PID, Reactome, WikiPathways
Protein Domains interpro Protein domain information, e.g., Serine/threonine-protein kinase, ATP binding site
Protein Structure pdb Multiple PDB structure identifiers for CDK2
Pharmaceutical Data pharmgkb PA101
Proteomics refseq Reference sequence identifiers for genomic, protein, and RNA
translation Protein to RNA translation mappings
Gene Information summary Brief gene description
map_location 12q13.2
Protein Interactions ipi IPI identifiers
Transcript Information exons Genomic exon positions for various transcripts
exons_hg19 Exon positions in HG19 genome version
transcript Associated transcripts, e.g., ENST00000266970.4
Gene Function Information generif PubMed-based gene references for functional studies
pubmed PubMed IDs
text Description of study findings
Evolutionary Data homologene Homologene gene entries
id 74409
genes Multiple homologous genes
Protein Family pantherdb PANTHER family information
Experimental Data reagent Experimental reagents (siRNA, shRNA, etc.) used for the gene
Wikipedia Information wikipedia URL: Cyclin-dependent kinase 2
Protein Interactions reporter Gene expression array probe identifiers
UniProt Data uniprot Swiss-Prot: P24941, TrEMBL: multiple entries
unii IEQ8K30M47

Example Variant querying results

Here is a table summarizing the key categories and fields from the given JSON file:

Category Field Value/Description
General Information _id chr7:g.55241707G>T
_version 2
Variant Type type SNV (Single Nucleotide Variant)
ref G
alt T
chrom 7
pos 55241707
rsid rs28929495
observed true
CADD Scores cadd.phred 26.2
cadd.annotype CodingTranscript
cadd.bstatistic 822
cadd.consdetail missense
cadd.consequence NON_SYNONYMOUS
cadd.gc 0.57
Gene Information cadd.gene.genename EGFR
cadd.gene.ccds_id CCDS5514.1
cadd.gene.feature_id ENST00000275493
cadd.gene.gene_id ENSG00000146648
cadd.gene.cds.cds_pos 2155
cadd.gene.prot.protpos 719
Protein Change clinvar.hgvs.protein Various entries, e.g., NP_001333827.1:p.Gly719Cys
cadd.oaa G (Original Amino Acid)
cadd.naa C (New Amino Acid)
cgi.protein_change EGFR:G719C
Clinical Information clinvar.rcv[].clinical_significance Various entries: drug response, Pathogenic, Likely pathogenic
clinvar.rcv[].conditions.name Various entries: Nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, somatic
clinvar.rcv[].origin somatic
Drug Response cgi[].association Responsive
cgi[].drug Various entries: HSP90 inhibitors, EGFR TK inhibitors, Afatinib, Gefitinib
cgi[].primary_tumor_type Various entries: Lung, Non-small cell lung
cgi[].evidence_level Various entries: FDA guidelines, Early trials, NCCN guidelines
Functional Annotations dbnsfp.aa.alt C
dbnsfp.appris principal1
dbnsfp.eigen.raw_coding 0.953480363944939
Pathogenicity Predictions polyphen.cat probably_damaging
polyphen.val 0.998
sift.cat deleterious
sift.val 0
Conservation Scores gerp.rs 387.1
phylop.mammalian 2.742
phast_cons.mammalian 1.0
fitcons 0.604399
Regulatory Annotations cadd.encode.h3k27ac 2.48
cadd.encode.exp 341.62
cadd.encode.nucleo 1.8
cadd.mapability.20bp 1
Pharmacogenomics clinvar.rcv[].conditions.identifiers Various entries, e.g., medgen: C4016032, mondo: MONDO:0005233
Publications dbsnp.citations Various PubMed IDs: 15118073, 15329413
docm.pubmed_id 15118073, 19922469
mutdb.cosmic_id 20881, 6253
clinvar.variant_id 16611

Documentation and Community

For detailed documentation and usage examples, visit BioThings.io Documentation. The community is active and provides support through forums, tutorials, and GitHub repositories.

Conclusion

BioThings.io offers a comprehensive suite of annotation services for researchers and bioinformaticians, enabling easy access to high-quality data for genes, variants, chemicals, and diseases. Its APIs are built to be fast, scalable, and easy to integrate, making it a valuable resource for a wide range of biomedical research applications.