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dbxref.txt
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________________________________________________________________________________
description: Databases cross-referenced in HTS-CSRS Biocompute Objects
title: dbxref.txt
Release: Oct-03-2016
--------------------------------------------------------------------------------
High-Throughput Sequencing Computational Standards for Regulatory Sciences
(HTS-CSRS) Knowlegebase.
--------------------------------------------------------------------------------
George Washington University Washington, DC, USA
US Food and Drug Administration (FDA) Silverspring, MD, USA
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NOTES:
id : id number - db object number
name : Abreviation used for that db
title : Full name of db
reference : PubMed and DOI reference (paper)
serverDomain : host URL
recordUrl : URL for accessing data programmatically
description : Description of db
--------------------------------------------------------------------------------
This document lists all the databases that are cross referenced in HTS-CSRS.
The databases that are specifically mentioned in the "web resource"
comment topic of HTS-CSRS are not listed.
Databases are listed in XR lines which are used as resources for information
related to biocompute entries and are found in resources other than HTS-CSRS.
The recordUrl field allows to access an entry in the cross referenced
database by substituting the '%s' in the url with an object ID from that DB.
--------------------------------------------------------------------------------
id : DBN.0100
name : HIVE
title : High-performance integrated virtual environment
reference : PMID=26989153; DOI=10.1093/database/baw022
serverDomain : https://hive.biochemistry.gwu.edu/
recordUrl : https://hive.biochemistry.gwu.edu/dna.cgi?cmd=propget&ids=%s&raw=1&mode=json
description : HIVE is a cloud-based environment optimized for the storage and analysis of extra-large data.
id : DBN.0200
name : GO
title : Gene Ontology Consortium
reference : PMID:10802651
serverDomain : http://geneontology.org/
recordUrl : http://amigo.geneontology.org/amigo/medial_search?q=%s
description : Gene ontology database
id : DBN.0300
name : NucCore
title : Nucleotide
reference : PMID:26590407
serverDomain : http://www.ncbi.nlm.nih.gov/nuccore
recordUrl : http://www.ncbi.nlm.nih.gov/nuccore/?term=%s
description : Sequence database of all publicly available DNA sequences
id : DBN.0400
name : DO
title : Disease-Ontology, standardized ontology for human disease
reference : PMID:25348409
serverDomain : http://disease-ontology.org/
recordUrl : http://disease-ontology.org/
description : Disease specific database
id : DBN.0500
name : ICD
title : International Classification of Disease (Tenth Edition)
reference : PMID:24480646
serverDomain : http://www.icd10data.com/
recordUrl : http://www.icd10data.com/Search.aspx?search=%s
description : A database that consists of all clinical codes
id : DBN.0600
name : SRA
title : Sequence Read Archive
reference : PMID:21062823
serverDomain : http://www.ncbi.nlm.nih.gov/sra
recordUrl : http://www.ncbi.nlm.nih.gov/sra/?term=%s
description : A database that stores raw sequencing data and alignment
information
id : DBN.0700
name : KEGG
title : Kyoto Encyclopedia of Genes and Genomes
reference : PMID:9847135
serverDomain : http://www.genome.jp/kegg/
recordUrl : http://www.genome.jp/dbget-bin/www_bfind_sub?mode=bfind&max_hit=1000&dbkey=kegg&keywords=%s
description : A database resource for understanding high-level and utilities of the biological system
id : DBN.0800
name : OMIM
title : Online Mendalian Inheritance in Man
reference : PMID:1062823
serverDomain : http://www.ncbi.nlm.nih.gov/omim
recordUrl : http://www.ncbi.nlm.nih.gov/omim/?term=%s
description : Database of human genes and genetic phenotypes
id : DBN.0900
name : ORCID
title : Open Researcher and Contributor ID
reference : PMID:26952357
serverDomain : http://orcid.org/
recordUrl : https://orcid.org/orcid-search/quick-search?searchQuery=%s
description : Repository that stores codes that uniquely identify scientific and other academic authors and contributors
id : DBN.1000
name : SO
title : Sequence Ontology
reference : PMID:15892872
serverDomain : http://www.sequenceontology.org/
recordUrl : http://www.sequenceontology.org/browser/current_svn/term/%s
description : SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation.
id : DBN.1100
name : taxID
title : Taxonomy
reference : PMID: 26590407
serverDomain : http://www.ncbi.nlm.nih.gov/taxonomy
recordUrl : http://www.ncbi.nlm.nih.gov/taxonomy/?term=%s
description : Sequence database of all publicly available DNA sequences
id : DBN.1200
name : PubChem
title : PubChem Compound
reference : PMID:26400175
serverDomain : https://www.ncbi.nlm.nih.gov/pccompound
recordUrl : https://pubchem.ncbi.nlm.nih.gov/compound/%s
description : The PubChem Compound Database contains validated chemical depiction information provided to describe substances in PubChem Substance.
id : DBN.1300
name : UBERON
title : Uberon
reference : PMID: 22293552
serverDomain : http://www.ebi.ac.uk/ols/
recordUrl : http://www.ebi.ac.uk/ols/search?q=%S&submit=Search+Uberon&ontology=uberon
description : Uberon is an integrated cross-species ontology covering anatomical structures in animals.
________________________________________________________________________________