v1.6
An integrated data warehouse for the Bovine Genome Database
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Given a gene id or gene symbol, retrieve the chromosomal coordinates.
Given a gene id or symbol, retrieve GO terms. Be sure to view the Qualifier column for genes annotated as "NOT".
Given a SNP rsID, retrieve ids (AnimalQTLdb) of overlapping QTL and traits.
Given a chromosome id and coordinates, retrieve genes.
Given a Gene id, retrieve expression values, metadata and BRENDA Tissue Ontology.
Given a bovine SNP rsID, retrieve chromosome location.
Given a bovine SNP rsID, retrieve gene. No rows will be returned if the SNP is not within a gene.
Given a gene id or symbol, retrieve pathways. The pathway data sources retrieved may be affected by the input id (RefSeq, Ensembl or gene symbol).
Given a gene id, retrieve variants and their consequences.
Given a chromosome id, retrieve genes and their locations.
Given a gene id or symbol, retrieve publications.
Given a GO term (e.g. DNA binding) or GO identifier (e.g. GO:0003677), retrieve genes. Wildcards (*) are allowed (e.g. *muscle*).
Given gene id or symbol, retrieve interacting genes.
Given a gene id or symbol in the selected organism, retrieve homologues. Optionally select homologue type.
Given a gene source (e.g. RefSeq or Ensembl), retrieve all gene ids. Use this to create a single-gene-set background list for enrichment.
Given a bovine trait, retrieve QTL id (AnimalQTLdb) and chromosomal location.
Given a gene id or symbol, retrieve transcript ids, locations and exon locations.
Given a gene id, retrieve proteins (UniProt) and protein domains.
Given a bovine SNP alias ID, such as ssID or an array id, retrieve dbSNP rsID.
Given an organism and gene set, retrieve all genes and their locations.
Given a gene id or symbol in the selected organism, retrieve GO terms and homologues. Optionally select homologue type.
Given an organism, retrieve all transcripts with genes and database cross references. Multiple gene sets may be retrieved, and can be filtered in the output.
Given a gene id or symbol, retrieve Reactome pathways.
Given a bovine dbSNP rsID, retrieve SNP Alias IDS and sources.
Given a gene id, retrieve database cross reference id (e.g. RefSeq to Ensembl or vice versa).
Given an organism, retrieve all protein ids (UniProt).
Given a bovine tissue, retrieve gene expression levels. Optionally constrain by gene expression cutoff and gene source.
Given a gene id in organism 1, retrieve homologues in organism 2 and pathways for the homologues. Optionally select homologue type.
Given a bovine QTL id (AnimalQTLdb), retrieve transcripts within QTL region. A list of transcripts can be saved and used in an expression template query. No rows will be returned if there are no transcripts.
Given a protein id (UniProt), retrieve genes and GO.
Given a gene id or symbol from the selected non-bovine organism, retrieve bovine homologues and pathways. Optionally select homologue type.
Given a gene id or symbol, retrieve homologues.
Given a gene id or gene symbol, retrieve proteins (UniProt).
Given a bovine Ensembl gene id or symbol, retrieve metabolic reactions and subsystems.
Given a non-human Gene id, retrieve human homologues and pathway information for those homologues. Optionally select homologue type.
Given a bovine QTL id (AnimalQTLdb) on the ARS_UCD1.2 assembly, retrieve genes within QTL region. You can create a gene list to use in a gene template query. No rows will be returned if there are no genes.
Given a bovine trait, retrieve QTL on the ARS-UCD1.2 assembly from AnimalQTLdb.
Given a QTL id from AnimalQTLdb, retrieve trait and Vertebrate Trait Ontology.
Given a protein id (UniProt), retrieve publications.
Given a bovine Ensembl gene id, retrieve ORIS (Orthology Inference Using Synteny) orthologues and orthologue cluster id.
Given a gene id or symbol, retrieve transcript ids and coding sequences.
Given a gene id, retrieve gene symbol and description.
Given a transcript id, retrieve gene id.
Given protein domain name (InterPro), retrieve information about protein domains. Wildcards (*) are allowed.
Given a transcript id, retrieve protein id (from gene set, not UniProt).
Given an organism, retrieve UniProt proteins with publications.
Given a gene id, retrieve transcript id(s).
Retrieve all gene ids and database cross reference ids for the specified organism and gene source.
Given a gene id or symbol in the selected organism, retrieve human orthologues.
Given a transcript ID, retrieve gene id and GO terms.
For a given organism, retrieve all mRNAs and proteins along with their lengths. All gene sources are provided.
Given a transcript id, retrieve gene id and pathways.
Given a gene id or symbol, retrieve transcript and protein ids (from the gene set, not UniProt).
Given an organism, retrieve all miRNAs and their locations.
Given a trait, retrieve VTO term. Remove trait name constraint to retrieve all traits and VTO terms.
Given an InterPro id, retrieve proteins and genes.
Given a gene alias id, retrieve gene id. This template should be used to convert RefSeq-UMD3.1.1 or RefSeq-Oarv3.1 gene ids to BovineMine gene ids for use in template queries that require gene ids.
Given a bovine QTL ID from AnimalQTLdb, retrieve SNPs within the QTL region.
Given a gene ID, retrieve database crossreference gene and locations of both. This is useful for comparing genes across assembly versions for B. taurus and O. aries. If the gene is from RefSeq of an older assembly (UMD3.1.1 or Oar_v3.1), you should append the assembly name to the gene id (e.g. 100048947-UMD3.1.1 or 100034665-Oar_v3.1).
Given a gene id, retrieve transcripts.
Given a gene source and organism, retrieve all gene ids, gene symbols and transcript ids.
Given a gene ID, retrieve database crossreference gene from a specified gene source and locations of both. This is useful for comparing genes across assembly versions for B. taurus and O. aries. If the gene is from RefSeq of an older assembly (UMD3.1.1 or Oar_v3.1), you should append the assembly name to the gene id (e.g. 100048947-UMD3.1.1 or 100034665-Oar_v3.1).
Given a gene symbol, retrieve gene id from the specified gene set.
Given a gene id, retrieve transcripts and proteins.
Given a protein id (UniProt), retrieve corresponding gene and location of gene.
Given a chromosome id and coordinates, retrieve miRNAs.
Given an InterPro protein domain name, retrieve proteins and genes for an organism. Wildcards (*) are allowed.
Given a genome assembly version, retrieve primary chromosome ids used in BovineMine and alternative ids.
Given a transcript id, retrieve protein id.
Given a gene id, retrieve publications.
Given a Bovine Ensembl95 transcript ID, retrieve non-synonymous coding variants.
