zhongwei/gh-k-dense-ai-claude-scientific-skills-scientific-skills

Files

Zhongwei Li f0bd18fb4e Initial commit

2025-11-30 08:30:10 +08:00

6.5 KiB

Raw Blame History

UniProt ID Mapping Databases

Complete list of databases supported by the UniProt ID Mapping service. Use these database names when calling the ID mapping API.

Retrieving Database List Programmatically

import requests
response = requests.get("https://rest.uniprot.org/configure/idmapping/fields")
databases = response.json()

UniProt Databases

UniProtKB

UniProtKB_AC-ID - UniProt accession and ID
UniProtKB - UniProt Knowledgebase
UniProtKB-Swiss-Prot - Reviewed (Swiss-Prot)
UniProtKB-TrEMBL - Unreviewed (TrEMBL)
UniParc - UniProt Archive
UniRef50 - UniRef 50% identity clusters
UniRef90 - UniRef 90% identity clusters
UniRef100 - UniRef 100% identity clusters

Sequence Databases

Nucleotide Sequence

EMBL - EMBL/GenBank/DDBJ
EMBL-CDS - EMBL coding sequences
RefSeq_Nucleotide - RefSeq nucleotide sequences
CCDS - Consensus CDS

Protein Sequence

RefSeq_Protein - RefSeq protein sequences
PIR - Protein Information Resource

Gene Databases

GeneID - Entrez Gene
Gene_Name - Gene name
Gene_Synonym - Gene synonym
Gene_OrderedLocusName - Ordered locus name
Gene_ORFName - ORF name

Genome Databases

General

Ensembl - Ensembl
EnsemblGenomes - Ensembl Genomes
EnsemblGenomes_PRO - Ensembl Genomes protein
EnsemblGenomes_TRS - Ensembl Genomes transcript
Ensembl_PRO - Ensembl protein
Ensembl_TRS - Ensembl transcript

Organism-Specific

KEGG - KEGG Genes
PATRIC - PATRIC
UCSC - UCSC Genome Browser
VectorBase - VectorBase
WBParaSite - WormBase ParaSite

Structure Databases

PDB - Protein Data Bank
AlphaFoldDB - AlphaFold Database
BMRB - Biological Magnetic Resonance Data Bank
PDBsum - PDB summary
SASBDB - Small Angle Scattering Biological Data Bank
SMR - SWISS-MODEL Repository

Protein Family and Domain Databases

InterPro - InterPro
Pfam - Pfam protein families
PROSITE - PROSITE
SMART - SMART domains
CDD - Conserved Domain Database
HAMAP - HAMAP
PANTHER - PANTHER
PRINTS - PRINTS
ProDom - ProDom
SFLD - Structure-Function Linkage Database
SUPFAM - SUPERFAMILY
TIGRFAMs - TIGRFAMs

Organism-Specific Databases

Model Organisms

MGI - Mouse Genome Informatics
RGD - Rat Genome Database
FlyBase - FlyBase (Drosophila)
WormBase - WormBase (C. elegans)
Xenbase - Xenbase (Xenopus)
ZFIN - Zebrafish Information Network
dictyBase - dictyBase (Dictyostelium)
EcoGene - EcoGene (E. coli)
SGD - Saccharomyces Genome Database (yeast)
PomBase - PomBase (S. pombe)
TAIR - The Arabidopsis Information Resource

Human-Specific

HGNC - HUGO Gene Nomenclature Committee
CCDS - Consensus Coding Sequence Database

Pathway Databases

Reactome - Reactome
BioCyc - BioCyc
PlantReactome - Plant Reactome
SIGNOR - SIGNOR
SignaLink - SignaLink

Enzyme and Metabolism

EC - Enzyme Commission number
BRENDA - BRENDA enzyme database
SABIO-RK - SABIO-RK (biochemical reactions)
MetaCyc - MetaCyc

Disease and Phenotype Databases

OMIM - Online Mendelian Inheritance in Man
MIM - MIM (same as OMIM)
OrphaNet - Orphanet (rare diseases)
DisGeNET - DisGeNET
MalaCards - MalaCards
CTD - Comparative Toxicogenomics Database
OpenTargets - Open Targets

Drug and Chemical Databases

ChEMBL - ChEMBL
DrugBank - DrugBank
DrugCentral - DrugCentral
GuidetoPHARMACOLOGY - Guide to Pharmacology
SwissLipids - SwissLipids

Gene Expression Databases

Bgee - Bgee gene expression
ExpressionAtlas - Expression Atlas
Genevisible - Genevisible
CleanEx - CleanEx

Proteomics Databases

PRIDE - PRIDE proteomics
PeptideAtlas - PeptideAtlas
ProteomicsDB - ProteomicsDB
CPTAC - CPTAC
jPOST - jPOST
MassIVE - MassIVE
MaxQB - MaxQB
PaxDb - PaxDb
TopDownProteomics - Top Down Proteomics

Protein-Protein Interaction

STRING - STRING
BioGRID - BioGRID
IntAct - IntAct
MINT - MINT
DIP - Database of Interacting Proteins
ComplexPortal - Complex Portal

Ontologies

GO - Gene Ontology
GeneTree - Ensembl GeneTree
HOGENOM - HOGENOM
HOVERGEN - HOVERGEN
KO - KEGG Orthology
OMA - OMA orthology
OrthoDB - OrthoDB
TreeFam - TreeFam

Other Specialized Databases

Glycosylation

GlyConnect - GlyConnect
GlyGen - GlyGen

Protein Modifications

PhosphoSitePlus - PhosphoSitePlus
iPTMnet - iPTMnet

Antibodies

Antibodypedia - Antibodypedia
DNASU - DNASU

Protein Localization

COMPARTMENTS - COMPARTMENTS
NeXtProt - NeXtProt (human proteins)

Evolution and Phylogeny

eggNOG - eggNOG
GeneTree - Ensembl GeneTree
InParanoid - InParanoid

Technical Resources

PRO - Protein Ontology
GenomeRNAi - GenomeRNAi
PubMed - PubMed literature references

Common Mapping Scenarios

Example 1: UniProt to PDB

from_db = "UniProtKB_AC-ID"
to_db = "PDB"
ids = ["P01308", "P04637"]

Example 2: Gene Name to UniProt

from_db = "Gene_Name"
to_db = "UniProtKB"
ids = ["BRCA1", "TP53", "INSR"]

Example 3: UniProt to Ensembl

from_db = "UniProtKB_AC-ID"
to_db = "Ensembl"
ids = ["P12345"]

Example 4: RefSeq to UniProt

from_db = "RefSeq_Protein"
to_db = "UniProtKB"
ids = ["NP_000207.1"]

Example 5: UniProt to GO Terms

from_db = "UniProtKB_AC-ID"
to_db = "GO"
ids = ["P01308"]

Usage Notes

Database names are case-sensitive: Use exact names as listed
Many-to-many mappings: One ID may map to multiple target IDs
Failed mappings: Some IDs may not have mappings; check the failedIds field in results
Batch size limit: Maximum 100,000 IDs per job
Result expiration: Results are stored for 7 days
Bidirectional mapping: Most databases support mapping in both directions

API Endpoints

Get available databases

GET https://rest.uniprot.org/configure/idmapping/fields

Submit mapping job

POST https://rest.uniprot.org/idmapping/run
Content-Type: application/x-www-form-urlencoded

from={from_db}&to={to_db}&ids={comma_separated_ids}

Check job status

GET https://rest.uniprot.org/idmapping/status/{jobId}

Get results

GET https://rest.uniprot.org/idmapping/results/{jobId}

Resources

ID Mapping tool: https://www.uniprot.org/id-mapping
API documentation: https://www.uniprot.org/help/id_mapping
Programmatic access: https://www.uniprot.org/help/api_idmapping

6.5 KiB Raw Blame History