v1.5
An integrated data warehouse for the Hymenoptera Genome Database
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Please contact us if you would like any additional template queries or if you have a concern about a query not completing.
Given a gene id, retrieve the coding sequences.
Retrieve gene ids and their aliases for an organism. Multiple gene sets may be returned if the gene source is not selected. See the Data Source page for gene source names.This template can be used for A. dorsata, A. florea, A. mellifera, B. impatiens, B. terrestris, L. humile, P. barbatus, W. auropuncata.
Given a gene id, retrieve GO terms.
Given a Gene id retrieve transcript id(s). This is especially useful for RefSeq gene sets,
Given a UniProt id, retrieve gene id.
Given an Alias ID, retrieve Gene ID, optionally constrained by gene source. This template can be used for A. dorsata, A. florea, A. mellifera, B. impatiens, B. terrestris, L. humile, P. barbatus, W. auropuncata.
Given a gene id, retrieve homologues from the OrthoDB and or HGD-Ortho datasets. Optionally constrain the homologues to a selected organism. By default the Last Common Ancestor is set to Holometabola, the broadest taxonomic group in HGD. If your output has inparalogs (multiple homologous genes per species), narrowing the taxonomic group may reduce the number of inparalogs. Depending on the input species and the taxonomic group selected, the results may include both HGD-Ortho and OrthoDB datasets, which can be filtered from the output table.
Given a gene id or symbol, retrieve transcript ids and locations and exon coordinates.
Given a gene id or symbol, retrieve chromosome and coordinates.
Retrieve all homologues for an organism. By default the Last Common Ancestor is set to Holometabola, the broadest taxonomic group in HGD, but you can modify it using the pulldown menu. The output may include both HGD-Ortho and OrthoDB datasets, which can be filtered.
Given a gene id, retrieve gene symbol and description.
Given a gene symbol, retrieve proteins (UniProt).
Retrieve gene ids and UniProt protein ids from a gene set. Multiple gene sets will be retrieved for organisms that have more than one gene set, unless the optional constraint to specify gene set is used. Output will include only ids that correspond to a UniProt id.
Given a Gene Symbol, retrieve GO terms.
Given the gene source and organism, retrieve all gene ids. This template is useful for creating a whole-gene-set background population for the enrichment widgets if you save the output as a list.
Given a gene id, retrieve gene alias id. This template can be used for A. dorsata, A. florea, A. mellifera, B. impatiens, B. terrestris, L. humile, P. barbatus, W. auropuncata.
Given a Gene ID, retrieve homologues from the selected organism and their pathways. A homologue will not be listed if it does not have a pathway. By default the Last Common Ancestor is set to Holometabola, the broadest taxonomic group in HGD. If your output has inparalogs (multiple homologous genes per species), narrowing the taxonomic group may reduce the number of inparalogs. Depending on the input species and the taxonomic group selected, the results may include both HGD-Ortho and OrthoDB datasets, which can be filtered from the output table.
Given a gene symbol, retrieve gene id.
Given a gene id, retrieve pathways.
Given an orthologue cluster id from OrthoDB or HGD-Ortho, retrieve all gene relationships in the cluster.
For a given organism, retrieve gene ids from the selected gene set mapped to UniProt protein ids. Only gene ids that map to UniProt ids will be retrieved. Mappings are from UniProt.
Given a GO term, retrieve genes annotated with that GO Term for a selected organism.
Given a non-A.mellifera organism, retrieve all A. mellifera orthologues with their pathways.
Given a gene id, retrieve gene symbol and go terms.
Retrieve all gene symbols and descriptions from a RefSeq gene set for a specified organism.
Retrieve genes located on a chromosome for an organism.
Given a gene alias id, retrieve genes and gene database cross references. This is useful for converting from old to new OGS. This template can be used for A. dorsata, A. florea, A. mellifera, B. impatiens, B. terrestris, L. humile, P. barbatus, W. auropuncata.
Given a gene id, retrieve database cross reference id.
Given a gene symbol and organism, retrieve homologues and GO terms of homologues.
Retrieve all proteins (UniProt) for a particular organism.
Given a Gene ID, retrieve Drosophila melanogaster homologues.
Given a Gene ID, retrieve Drosophila melanogaster homologues and their Reactome pathways. A homologue will not be listed if it does not have a Reactome pathway. Depending on the species of the input gene, the results may include both HGD-Ortho and OrthoDB datasets, which can be filtered from the output table.
Given a CDS ID, retrieve gene id and symbol. This is useful for a list of CDS retrieved from a regions search.
Given a RefSeq or GenBank protein id, retrieve protein sequences.
Given a Gene ID, retrieve Drosophila melanogaster homologues and their GO terms. A homologue will not be listed if it does not have any GO terms. Depending on the species of the input gene, the results may include both HGD-Ortho and OrthoDB datasets, which can be filtered from the output table.
Given a transcript id, retrieve transcript alias id.
Given a gene id, retrieve gene alias ids and database cross references. This template can be used for A. dorsata, A. florea, A. mellifera, B. impatiens, B. terrestris, L. humile, P. barbatus, W. auropuncata.
Given an organism, retrieve all transcript ids with their gene ids and alias ids. Multiple gene sets may be retrieved if the optional gene source constraint is not selected. This template can be used for A. dorsata, A. florea, A. mellifera, B. impatiens, B. terrestris, L. humile, P. barbatus, W. auropuncata.
Given an OGS gene id, retrieve database cross reference id (RefSeq) with symbols and descriptions.
Given a NCBI gene ID, retrieve protein and coding sequences.
Given a transcript ID, retrieve gene ID and symbol.
Given a transcript alias id, retrieve transcript and gene id. This template should be used for A. echinatior, C. biroi, C. floridanus, D. novaeangliae, E. Mexicana, H. laboriosa, H. saltator, L. albipes, M. quadrifasciata, M. rotundata, S. invicta.
Given an organism, retrieve all genes that have go terms, along with their GO terms.
Retrieve all genes and their chromosomal locations for an organism.
Retrieve gene ids for an organism. Multiple gene sets may be returned if the gene source is not selected. See the Data Source page for gene source names.
Given an organism, retrieve gene ids that have pathways, along with their pathways.
Retrieve all publications with gene ids from an organism.
Given a gene id, retrieve publications.
Given a gene id, retrieve transcript ids and protein ids from the gene source.
Given a gene id, retrieve homologues from the selected organism and their GO terms. A homologue will not be listed if it does not have any GO terms. By default the Last Common Ancestor is set to Holometabola, the broadest taxonomic group in HGD. If your output has inparalogs (multiple homologous genes per species), narrowing the taxonomic group may reduce the number of inparalogs. Depending on the input species and the taxonomic group selected, the results may include both HGD-Ortho and OrthoDB datasets, which can be filtered from the output table.
Given a genome assembly version, retrieve primary chromosome IDs used in HymenopteraMine, alternative IDs and chromosome lengths. In the results table, the ID that should be used in the Regions Search is called "DB Identifier".
Given a RefSeq or GenBank gene id, retrieve associated protein sequences (from RefSeq or GenBank).
Given a transcript id, retrieve transcript alias id. This template can be used for A. echinatior, C. biroi, C. floridanus, D. novaeangliae, E. Mexicana, H. laboriosa, H. saltator, L. albipes, M. quadrifasciata, M. rotundata, S. invicta.
Given a transcript id from RefSeq or GenBank, retrieve the coding sequence.
Given a transcript alias id, retrieve primary transcript id and gene id, gene database cross reference id, and gene description. This template can be used for A. echinatior, C. biroi, C. floridanus, D. novaeangliae, E. Mexicana, H. laboriosa, H. saltator, L. albipes, M. quadrifasciata, M. rotundata, S. invicta.
Given a Gene ID, retrieve Drosophila melanogaster homologues and their KEGG pathways. A homologue will not be listed if it does not have a KEGG pathway. Depending on the species of the input gene, the results may include both HGD-Ortho and OrthoDB datasets, which can be filtered from the output table.
