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Database Commons - CARLSBAD

CARLSBAD

Citations: 5

z-index 0.98

Short name CARLSBAD
Full name
Description CARLSBAD is a confederated database of chemical bioactivities.
URL http://carlsbad.health.unm.edu/carlsbad/
Year founded 2013
Last update & version NA    v1.0
Availability Free to all users
University/Institution hosted University of New Mexico
Address MSC09 5025, Albuquerque, NM 87131, USA
City Albuquerque
Province/State
Country/Region United States
Contact name Tudor I. Oprea
Contact email toprea@salud.unm.edu
Data type(s)
Major organism(s)
Keyword(s)
  • chemical bioactivity
Publication(s)
  • The CARLSBAD database: a confederated database of chemical bioactivities. [PMID: 23794735]

    Stephen L Mathias, Jarrett Hines-Kay, Jeremy J Yang, Gergely Zahoransky-Kohalmi, Cristian G Bologa, Oleg Ursu, Tudor I Oprea
    Database : the journal of biological databases and curation 2013:2013
    5 Citations (Google Scholar as of 2016-01-29)

    Abstract: Many bioactivity databases offer information regarding the biological activity of small molecules on protein targets. Information in these databases is often hard to resolve with certainty because of subsetting different data in a variety of formats; use of different bioactivity metrics; use of different identifiers for chemicals and proteins; and having to access different query interfaces, respectively. Given the multitude of data sources, interfaces and standards, it is challenging to gather relevant facts and make appropriate connections and decisions regarding chemical-protein associations. The CARLSBAD database has been developed as an integrated resource, focused on high-quality subsets from several bioactivity databases, which are aggregated and presented in a uniform manner, suitable for the study of the relationships between small molecules and targets. In contrast to data collection resources, CARLSBAD provides a single normalized activity value of a given type for each unique chemical-protein target pair. Two types of scaffold perception methods have been implemented and are available for datamining: HierS (hierarchical scaffolds) and MCES (maximum common edge subgraph). The 2012 release of CARLSBAD contains 439 985 unique chemical structures, mapped onto 1,420 889 unique bioactivities, and annotated with 277 140 HierS scaffolds and 54 135 MCES chemical patterns, respectively. Of the 890 323 unique structure-target pairs curated in CARLSBAD, 13.95% are aggregated from multiple structure-target values: 94 975 are aggregated from two bioactivities, 14 544 from three, 7 930 from four and 2214 have five bioactivities, respectively. CARLSBAD captures bioactivities and tags for 1435 unique chemical structures of active pharmaceutical ingredients (i.e. 'drugs'). CARLSBAD processing resulted in a net 17.3% data reduction for chemicals, 34.3% reduction for bioactivities, 23% reduction for HierS and 25% reduction for MCES, respectively. The CARLSBAD database supports a knowledge mining system that provides non-specialists with novel integrative ways of exploring chemical biology space to facilitate knowledge mining in drug discovery and repurposing. Database URL: http://carlsbad.health.unm.edu/carlsbad/.

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Accessibility

Rate of accessibility:
HTTP status codeDate requested
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200 OK2017-11-28
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200 OK2017-11-17
200 OK2017-11-14
200 OK2017-11-10
200 OK2017-11-07
200 OK2017-11-03
200 OK2017-10-31
200 OK2017-10-27
200 OK2017-10-24
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200 OK2017-10-13
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200 OK2017-08-25
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200 OK2017-03-14
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200 OK2017-03-07
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200 OK2017-02-28
200 OK2017-02-24
200 OK2017-02-21
200 OK2017-02-17
200 OK2017-02-14
200 OK2017-02-10
200 OK2017-02-07
200 OK2017-02-03
200 OK2017-01-31
200 OK2017-01-27
200 OK2017-01-24
200 OK2017-01-20
200 OK2017-01-17
200 OK2017-01-13
200 OK2017-01-10
200 OK2017-01-06
200 OK2017-01-03
200 OK2016-12-30
200 OK2016-12-27
200 OK2016-12-23
200 OK2016-12-20
200 OK2016-12-16
200 OK2016-12-13
200 OK2016-12-09
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200 OK2016-12-02
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200 OK2016-10-21
200 OK2016-10-18
200 OK2016-10-14
200 OK2016-10-11
200 OK2016-10-07
200 OK2016-10-04
200 OK2016-09-30
200 OK2016-09-27
200 OK2016-09-23
200 OK2016-09-20
200 OK2016-09-16
200 OK2016-09-13
200 OK2016-09-09
200 OK2016-09-06
200 OK2016-09-02
200 OK2016-08-30
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200 OK2016-08-19
200 OK2016-08-16
200 OK2016-08-12
200 OK2016-08-09
200 OK2016-08-05
200 OK2016-08-02
200 OK2016-07-29
200 OK2016-07-26
200 OK2016-07-22
200 OK2016-07-19
200 OK2016-07-15
200 OK2016-07-12
200 OK2016-07-08
200 OK2016-07-05
200 OK2016-07-01
200 OK2016-06-28
200 OK2016-06-24
200 OK2016-06-21
200 OK2016-06-17
200 OK2016-06-14
200 OK2016-06-10
200 OK2016-06-07
200 OK2016-06-03
200 OK2016-05-31
200 OK2016-05-27
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-1 Failed2016-02-03
200 OK2016-02-01
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200 OK2016-01-29
200 OK2016-01-27
200 OK2016-01-25
200 OK2016-01-24
200 OK2016-01-22
200 OK2016-01-20
200 OK2016-01-18
200 OK2016-01-17
200 OK2016-01-15
200 OK2016-01-13
200 OK2016-01-11
200 OK2016-01-10
200 OK2016-01-08
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200 OK2016-01-04

Tags

Interaction and Network Standard, Ontology and Nomenclature
Homo sapiens Mus musculus Rattus norvegicus
chemical bioactivity

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Mengwei Li [2016-03-31]
    • Lina Ma [2015-12-31]
    • Mengwei Li [2015-11-30]
    • Mengwei Li [2015-06-27]
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