biobouncer checks 46 sources. Each table below gives a valid example
id, the checking modes a source 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:
is_valid_id("MONDO:0005148", source_db = "mondo")
#> [1] TRUEThe full table is also available in code, so you never have to guess a key or an example:
source_info()
#> # A tibble: 46 × 6
#> key name example modes species_aware version_aware
#> <chr> <chr> <chr> <chr> <lgl> <lgl>
#> 1 bto BRENDA Tissue Ontolo… BTO:00… patt… FALSE TRUE
#> 2 cdd CDD cd00029 patt… FALSE FALSE
#> 3 chebi ChEBI CHEBI:… patt… FALSE TRUE
#> 4 chembl ChEMBL CHEMBL… patt… FALSE FALSE
#> 5 cl Cell Ontology CL:000… patt… FALSE TRUE
#> 6 clinvar ClinVar VCV000… patt… FALSE FALSE
#> 7 complexportal Complex Portal CPX-21… patt… FALSE FALSE
#> 8 cosmic COSMIC COSM476 patt… FALSE FALSE
#> 9 dbsnp dbSNP rs7412 patt… FALSE FALSE
#> 10 doid Human Disease Ontolo… DOID:9… patt… FALSE TRUE
#> # ℹ 36 more rowsModes: pattern checks the shape offline,
cache checks existence against a pinned snapshot, and
remote checks existence against the live source. See
vignette("biobouncer") 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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
is_valid_id("RF00001", source_db = "rfam")