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biobouncer (Python)

Sources cookbook

samuelbharti/biobouncer

Sources cookbook¶

biobouncer checks 46 sources. Each row below gives a valid example id, the checking modes it supports, and whether it is species-aware. To check an id, pass the source key as source_db. The call is the same for every source:

import biobouncer as bg

bg.is_valid_id("MONDO:0005148", source_db="mondo")
# True

The full table is also available in code, so you never have to guess a key or an example:

for row in bg.source_info():
    print(row["key"], row["example"], row["modes"])

Modes: pattern checks the shape offline, cache checks existence against a pinned snapshot, and remote checks existence against the live source. See the guide for details.

Diseases¶

Source	`source_db`	Example	Modes	Species-aware
MONDO Disease Ontology. Cross-referenced disease terms from the Monarch Initiative.	`mondo`	`MONDO:0005148`	pattern, cache, remote	no
Human Disease Ontology. Human diseases, mapped to other disease vocabularies.	`doid`	`DOID:9352`	pattern, cache, remote	no
Experimental Factor Ontology. Diseases, traits, and measurements from the GWAS Catalog and Open Targets.	`efo`	`EFO:0000400`	pattern, cache, remote	no
Orphanet. Rare diseases.	`orphanet`	`ORPHA:558`	pattern, remote	no
NCI Thesaurus. Cancer and biomedical concepts.	`ncit`	`NCIT:C3224`	pattern, remote	no

Check any id in the group the same way:

bg.is_valid_id("MONDO:0005148", source_db="mondo")

Phenotypes and traits¶

Source	`source_db`	Example	Modes	Species-aware
Human Phenotype Ontology. Human phenotypic abnormalities used in clinical genetics.	`hp`	`HP:0001250`	pattern, cache, remote	no
Mammalian Phenotype Ontology. Mammalian phenotypes, common in mouse studies.	`mp`	`MP:0001262`	pattern, cache, remote	no
Phenotype And Trait Ontology. Qualities and traits, often composed with other ontologies.	`pato`	`PATO:0000001`	pattern, cache, remote	no

Check any id in the group the same way:

bg.is_valid_id("HP:0001250", source_db="hp")

Anatomy, cells, and tissues¶

Source	`source_db`	Example	Modes	Species-aware
Uberon. Cross-species anatomy.	`uberon`	`UBERON:0002107`	pattern, cache, remote	no
Cell Ontology. Cell types.	`cl`	`CL:0000236`	pattern, cache, remote	no
BRENDA Tissue Ontology. Tissues and cell lines from BRENDA.	`bto`	`BTO:0000759`	pattern, cache, remote	no

Check any id in the group the same way:

bg.is_valid_id("UBERON:0002107", source_db="uberon")

Organisms and taxa¶

Source	`source_db`	Example	Modes	Species-aware
NCBI Taxonomy. Organisms and other taxa.	`ncbitaxon`	`NCBITaxon:9606`	pattern, remote	no

Check any id in the group the same way:

bg.is_valid_id("NCBITaxon:9606", source_db="ncbitaxon")

Genes¶

Source	`source_db`	Example	Modes	Species-aware
HGNC gene symbols. Approved symbols. A withdrawn symbol maps to its successor.	`hgnc`	`TP53`	pattern, cache, remote	no
Ensembl. Ensembl gene, transcript, and protein ids. Species-aware.	`ensembl`	`ENSG00000139618`	pattern, remote	yes
Open Targets. A human Ensembl gene id checked against the Open Targets Platform for target coverage.	`opentargets`	`ENSG00000139618`	pattern, remote	no
RefSeq. NCBI RefSeq accessions, with an optional version.	`refseq`	`NM_000546.6`	pattern, remote	no

Check any id in the group the same way:

bg.is_valid_id("TP53", source_db="hgnc")

Variants¶

Source	`source_db`	Example	Modes	Species-aware
dbSNP. dbSNP reference SNP ids.	`dbsnp`	`rs7412`	pattern, remote	no
HGVS. HGVS sequence variant syntax, such as a coding substitution.	`hgvs`	`NM_004006.2:c.4375C>T`	pattern, remote	no
ClinVar. ClinVar variation, record, and submission accessions.	`clinvar`	`VCV000012345`	pattern, remote	no
COSMIC. COSMIC somatic mutation ids.	`cosmic`	`COSM476`	pattern	no

Check any id in the group the same way:

bg.is_valid_id("rs7412", source_db="dbsnp")

Proteins and structures¶

Source	`source_db`	Example	Modes	Species-aware
UniProt. UniProt protein accessions. Species-aware.	`uniprot`	`P04637`	pattern, remote	yes
UniParc. UniParc unique sequence identifiers.	`uniparc`	`UPI0000000001`	pattern, remote	no
PDB. Protein Data Bank structures.	`pdb`	`4HHB`	pattern, remote	no
Complex Portal. Macromolecular complexes.	`complexportal`	`CPX-2158`	pattern, remote	no

Check any id in the group the same way:

bg.is_valid_id("P04637", source_db="uniprot")

Protein families and domains¶

Source	`source_db`	Example	Modes	Species-aware
Pfam. Protein families and domains.	`pfam`	`PF00001`	pattern, remote	no
InterPro. Integrated protein families, domains, and sites.	`interpro`	`IPR000001`	pattern, remote	no
PROSITE. Protein patterns and profiles.	`prosite`	`PS00001`	pattern, remote	no
SMART. Protein domain accessions.	`smart`	`SM00248`	pattern, remote	no
PANTHER. Protein family accessions.	`panther`	`PTHR11003`	pattern, remote	no
CDD. Conserved Domain Database models.	`cdd`	`cd00029`	pattern, remote	no
PRINTS. Protein fingerprint accessions.	`prints`	`PR00001`	pattern, remote	no
NCBIfam. NCBIfam and TIGRFAM models.	`ncbifam`	`TIGR00001`	pattern, remote	no

Check any id in the group the same way:

bg.is_valid_id("PF00001", source_db="pfam")

Function, sequence, and enzymes¶

Source	`source_db`	Example	Modes	Species-aware
Gene Ontology. Gene Ontology terms for function, process, and component.	`go`	`GO:0006915`	pattern, cache, remote	no
Sequence Ontology. Sequence Ontology features.	`so`	`SO:0000704`	pattern, cache, remote	no
EC number. Enzyme Commission numbers.	`ec`	`1.1.1.1`	pattern	no
Evidence and Conclusion Ontology. Evidence types for annotations.	`eco`	`ECO:0000269`	pattern, remote	no

Check any id in the group the same way:

bg.is_valid_id("GO:0006915", source_db="go")

Chemicals and drugs¶

Source	`source_db`	Example	Modes	Species-aware
ChEBI. Chemical entities of biological interest.	`chebi`	`CHEBI:15377`	pattern, cache, remote	no
ChEMBL. Bioactive molecules.	`chembl`	`CHEMBL25`	pattern, remote	no
DrugBank. Drug accessions.	`drugbank`	`DB00001`	pattern	no
PharmGKB. Pharmacogenomics accessions.	`pharmgkb`	`PA267`	pattern	no
InChIKey. Hashed chemical structure keys.	`inchikey`	`BSYNRYMUTXBXSQ-UHFFFAOYSA-N`	pattern	no

Check any id in the group the same way:

bg.is_valid_id("CHEBI:15377", source_db="chebi")

Pathways¶

Source	`source_db`	Example	Modes	Species-aware
Reactome. Reactome pathways, reactions, and entities.	`reactome`	`R-HSA-68886`	pattern, remote	no
WikiPathways. Community-curated pathways.	`wikipathways`	`WP554`	pattern, remote	no

Check any id in the group the same way:

bg.is_valid_id("R-HSA-68886", source_db="reactome")

RNA families¶

Source	`source_db`	Example	Modes	Species-aware
Rfam. RNA families.	`rfam`	`RF00001`	pattern, remote	no
miRBase. Mature microRNAs.	`mirbase`	`MIMAT0000001`	pattern, remote	no
miRBase hairpins. MicroRNA hairpin precursors.	`mirbase_hairpin`	`MI0000001`	pattern, remote	no

Check any id in the group the same way:

bg.is_valid_id("RF00001", source_db="rfam")