| URL: | https://senselab.med.yale.edu/OrDB/ |
| Full name: | Olfactory Receptor DataBase |
| Description: | a central repository of olfactory receptor (OR) and olfactory receptor-like gene and protein sequences. |
| Year founded: | 2002 |
| Last update: | 2015-08-01 |
| Version: | 6.0 |
| Accessibility: |
Accessible
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| Country/Region: | United States |
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| University/Institution: | Texas Tech University |
| Address: | Center for Biotechnology and Genomics |
| City: | Lubbock |
| Province/State: | Texas |
| Country/Region: | United States |
| Contact name (PI/Team): | Chiquito Crasto |
| Contact email (PI/Helpdesk): | chiquito.crasto@ttu.edu |
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ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions. [PMID: 27694208]
We present here an exploration of the evolution of three well-established, web-based resources dedicated to the dissemination of information related to olfactory receptors (ORs) and their functional ligands, odorants. These resources are: the Olfactory Receptor Database (ORDB), the Human Olfactory Data Explorer (HORDE) and ODORactor. ORDB is a repository of genomic and proteomic information related to ORs and other chemosensory receptors, such as taste and pheromone receptors. Three companion databases closely integrated with ORDB are OdorDB, ORModelDB and OdorMapDB; these resources are part of the SenseLab suite of databases (http://senselab.med.yale.edu). HORDE (http://genome.weizmann.ac.il/horde/) is a semi-automatically populated database of the OR repertoires of human and several mammals. ODORactor (http://mdl.shsmu.edu.cn/ODORactor/) provides information related to OR-odorant interactions from the perspective of the odorant. All three resources are connected to each other via web-links.Database URL: http://senselab.med.yale.edu; http://genome.weizmann.ac.il/horde/; http://mdl.shsmu.edu.cn/ODORactor/. © The Author(s) 2016. Published by Oxford University Press. |
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Olfactory Receptor Database: a metadata-driven automated population from sources of gene and protein sequences. [PMID: 11752336]
The Olfactory Receptor Database (ORDB; http://senselab.med.yale.edu/senselab/ordb) is a central repository of olfactory receptor (OR) and olfactory receptor-like gene and protein sequences. To deal with the very large OR gene family, we have constructed an algorithm that automatically downloads sequences from web sources such as GenBank and SWISS-PROT into the database. The algorithm uses hypertext markup language (HTML) parsing techniques that extract information relevant to ORDB. The information is then correlated with the metadata in the ORDB knowledge base to encode the unstructured text extracted into the structured format compliant with the database architecture, entity attribute value with classes and relationship (EAV/CR), which supports the SenseLab project as a whole. Three population methods: batch, automatic and semi-automatic population are discussed. The data is imported into the database using extensible markup language (XML). |