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H '''Comparative Toxicogenomics Database''' ('''CTD''') είναι μια δημόσια ιστοσελίδα και ένα εργαλείο έρευνας που ξεκίνησε το Νοέμβριο του 2004, το οποίο επιμελείται επιστημονικά δεδομένα που περιγράφουν τις σχέσεις μεταξύ χημικών ουσιών/φαρμάκων, γονιδίων/πρωτεϊνών, νόσων, ταξινομικών βαθμίδων, φαινοτύπων, οντολογίας γονιδίων (GO annotations), οδών και τύπων αλληλεπίδρασης.
H '''Comparative Toxicogenomics Database''' ('''CTD''') είναι μια δημόσια ιστοσελίδα και ένα εργαλείο έρευνας που ξεκίνησε το Νοέμβριο του 2004, το οποίο επιμελείται επιστημονικά δεδομένα που περιγράφουν τις σχέσεις μεταξύ χημικών ουσιών/φαρμάκων, γονιδίων/πρωτεϊνών, νόσων, ταξινομικών βαθμίδων, φαινοτύπων, οντολογίας γονιδίων (GO annotations), οδών και τύπων αλληλεπίδρασης.
Η βάση δεδομένων συντηρείται από το Τμήμα Βιολογικών Επιστημών στο Πολιτειακό Πανεπιστήμιο της Βόρειας Καρολίνα [[North Carolina State University]].
Η βάση δεδομένων συντηρείται από το Τμήμα Βιολογικών Επιστημών στο Πολιτειακό Πανεπιστήμιο της Βόρειας Καρολίνα [[North Carolina State University]].
==Background==
The Comparative Toxicogenomics Database (CTD) is a public website and research tool that curates scientific data describing relationships between chemicals, genes/proteins, diseases, taxa, phenotypes, GO annotations, pathways, and interaction modules, launched on November 12, 2004.<ref>{{cite journal |vauthors=Mattingly CJ, Rosenstein MC, Colby GT, Forrest JN, Boyer JL |title=The Comparative Toxicogenomics Database (CTD): A Resource for Comparative Toxicological Studies |journal=Journal of Experimental Zoology Part A: Comparative Experimental Biology |volume=305 |issue=9 |pages=689–92 |date=Sep 2006 |pmid=16902965 |pmc=1586110 |doi=10.1002/jez.a.307 }}</ref><ref>{{cite journal |vauthors=Mattingly CJ, Rosenstein MC, Davis AP, Colby GT, Forrest JN, Boyer JL |title=The Comparative Toxicogenomics Database (CTD): A Cross-Species Resource for Building Chemical-Gene Interaction Networks |journal=Toxicol. Sci. |volume=92 |issue=2 |pages=587–95 |date=Aug 2006 |pmid=16675512 |pmc=1586111 |doi=10.1093/toxsci/kfl008 }}</ref><ref>{{cite journal |vauthors=Mattingly CJ, Colby GT, Rosenstein MC, Forrest JN, Boyer JL |title=Promoting comparative molecular studies in environmental health research: an overview of the comparative toxicogenomics database (CTD) |journal=Pharmacogenomics J. |volume=4 |issue=1 |pages=5–8 |year=2004 |pmid=14735110 |doi=10.1038/sj.tpj.6500225 |doi-access=free }}</ref><ref>{{cite journal |vauthors=Mattingly CJ, Colby GT, Forrest JN, Boyer JL |title=The Comparative Toxicogenomics Database (CTD) |journal=Environ. Health Perspect. |volume=111 |issue=6 |pages=793–5 |date=May 2003 |pmid=12760826 |pmc=1241500 |url=http://ehp.niehs.nih.gov/txg/docs/2003/6028/abstract.html |doi=10.1289/ehp.6028 |url-status=dead |archiveurl=https://web.archive.org/web/20100606135634/http://ehp.niehs.nih.gov/txg/docs/2003/6028/abstract.html |archivedate=2010-06-06 }}</ref>
The database is maintained by the Department of Biological Sciences at North Carolina State University.{{citation needed|date=October 2016}}

==Goals and objectives==
One of the primary goals of CTD is to advance the understanding of the effects of environmental chemicals on human health on the genetic level, a field called [[toxicogenomics]].

The [[etiology]] of many chronic diseases involves interactions between environmental factors and genes that modulate important physiological processes. Chemicals are an important component of the environment. Conditions such as [[asthma]], cancer, [[diabetes mellitus|diabetes]], [[hypertension]], [[immunodeficiency]], and [[Parkinson's disease]] are known to be influenced by the environment; however, the molecular mechanisms underlying these correlations are not well understood. CTD may help resolve these mechanisms. The most up-to-date extensive list of peer-reviewed scientific articles about CTD is available at their publications page<ref>[http://ctdbase.org/about/publications/#ctdpubs CTD Publications page] ctdbase.org</ref>

==Core data==
CTD is a unique resource where [[biocurator]]s<ref>{{cite journal |vauthors=Bourne PE, McEntyre J |title=Biocurators: Contributors to the World of Science |journal=PLOS Comput. Biol. |volume=2 |issue=10 |pages=e142 |date=Oct 2006 |pmid=17411327 |pmc=1626157 |doi=10.1371/journal.pcbi.0020142 |bibcode=2006PLSCB...2..142B }}</ref><ref>{{cite journal |vauthors=Salimi N, Vita R |title=The Biocurator: Connecting and Enhancing Scientific Data |journal=PLOS Comput. Biol. |volume=2 |issue=10 |pages=e125 |date=Oct 2006 |pmid=17069454 |pmc=1626147 |doi=10.1371/journal.pcbi.0020125 |bibcode=2006PLSCB...2..125S }}</ref> read the scientific literature and manually curate four types of core data:

* Chemical-gene interactions
* Chemical-disease associations
* Gene-disease associations
* Chemical-phenotype associations

==Data integration==
By integrating the above four data sets, CTD automatically constructs putative chemical-gene-phenotype-disease networks to illuminate molecular mechanisms underlying environmentally-influenced diseases.

These inferred relationships are statistically scored and ranked and can be used by scientists and computational biologists to generate and verify testable hypotheses about toxicogenomic mechanisms and how they relate to human health.

Users can search CTD to explore scientific data for chemicals, genes, diseases, or interactions between any of these three concepts. Currently,{{when|date=November 2015}} CTD integrates toxicogenomic data for vertebrates and invertebrates.

CTD integrates data from or hyperlinks to these databases:
*ChemIDplus, a dictionary of more than 400,000 chemicals housed in the US National Library of Medicine<ref>[http://chem.sis.nlm.nih.gov/chemidplus/chemidlite.jsp ChemIDplus] US National Library of Medicine, n.d.,retrieved 7 November 2015</ref>
*[[DrugBank]]
*Data Infrastructure for Chemical Safety project (diXa) Data Warehouse by the European Bioinformatics Institute<ref>[http://wwwdev.ebi.ac.uk/fg/dixa/index.html diXa Data Warehouse] n.d., retrieved 7 November 2015</ref><ref>{{cite journal|last1=Hendrickx|first1=D. M.|last2=Aerts|first2=H. J. W. L.|last3=Caiment|first3=F.|last4=Clark|first4=D.|last5=Ebbels|first5=T. M. D.|last6=Evelo|first6=C. T.|last7=Gmuender|first7=H.|last8=Hebels|first8=D. G. A. J.|last9=Herwig|first9=R.|last10=Hescheler|first10=J.|last11=Jennen|first11=D. G. J.|last12=Jetten|first12=M. J. A.|last13=Kanterakis|first13=S.|last14=Keun|first14=H. C.|last15=Matser|first15=V.|last16=Overington|first16=J. P.|last17=Pilicheva|first17=E.|last18=Sarkans|first18=U.|last19=Segura-Lepe|first19=M. P.|last20=Sotiriadou|first20=I.|last21=Wittenberger|first21=T.|last22=Wittwehr|first22=C.|last23=Zanzi|first23=A.|last24=Kleinjans|first24=J. C. S.|title=diXa: a data infrastructure for chemical safety assessment|journal=Bioinformatics|date=12 December 2014|volume=31|issue=9|pages=1505–1507|doi=10.1093/bioinformatics/btu827|pmid=25505093|pmc=4410652}}</ref> which as of November 2015 contained 469 compounds, 188 disease datasets in three sub-categories liver, kidney and cardiovascular disease.<ref>[http://www.ebi.ac.uk/training/online/course/dixa-data-warehouse-exploring-data-toxicogenomics/studies-analyses-and-disease-data/disease-d Train online, Disease data] European Molecular Biology Laboratory,n.d.,retrieved 7 November 2015</ref>
*[[Gene Ontology|Gene Ontology Consortium]]
*[[KEGG]]
*[[Entrez|NCBI Entrez-Gene]]
*[[PubMed|NCBI PubMed]]
*NCBI Taxonomy<ref>[https://www.ncbi.nlm.nih.gov/sites/entrez?db=taxonomy NCBI Taxonomy]</ref>
*[[Medical Subject Headings|NLM Medical Subject Headings]]
*[[Mendelian Inheritance in Man|OMIM]]
*[[Reactome]]

==References==
{{reflist|30em}}

==External links==
* [http://ctdbase.org/ Comparative Toxicogenomics Database]
* [http://www.mdibl.org/ MDI Biologicjfxal Laboratory]

[[Category:Genetics databases]]
[[Category:Ontology (information science)]]
[[Category:Toxicology]]
[[Category:Chemical databases]]
[[Category:Molecular genetics]]
[[Category:Environmental science]]
[[Category:Comparisons]]

Έκδοση από την 12:05, 23 Δεκεμβρίου 2021

Συγκριτική Τοξικογονιδιωματική βάση δεδομένων
Γενικά
Είδοςλογισμικό, βάση δεδομένων που αφορά τη βιολογία, βάση δεδομένων που αφορά την χημεία
Διανομή
Λειτουργικά
Διαθέσιμο σεΑγγλικά
Ανάπτυξη
Άδεια χρήσηςιδιόκτητη άδεια
Σύνδεσμοι
Επίσημος ιστότοπος
http://ctdbase.org/

H Comparative Toxicogenomics Database (CTD) είναι μια δημόσια ιστοσελίδα και ένα εργαλείο έρευνας που ξεκίνησε το Νοέμβριο του 2004, το οποίο επιμελείται επιστημονικά δεδομένα που περιγράφουν τις σχέσεις μεταξύ χημικών ουσιών/φαρμάκων, γονιδίων/πρωτεϊνών, νόσων, ταξινομικών βαθμίδων, φαινοτύπων, οντολογίας γονιδίων (GO annotations), οδών και τύπων αλληλεπίδρασης. Η βάση δεδομένων συντηρείται από το Τμήμα Βιολογικών Επιστημών στο Πολιτειακό Πανεπιστήμιο της Βόρειας Καρολίνα North Carolina State University.

Background

The Comparative Toxicogenomics Database (CTD) is a public website and research tool that curates scientific data describing relationships between chemicals, genes/proteins, diseases, taxa, phenotypes, GO annotations, pathways, and interaction modules, launched on November 12, 2004.[1][2][3][4] The database is maintained by the Department of Biological Sciences at North Carolina State University.[εκκρεμεί παραπομπή]

Goals and objectives

One of the primary goals of CTD is to advance the understanding of the effects of environmental chemicals on human health on the genetic level, a field called toxicogenomics.

The etiology of many chronic diseases involves interactions between environmental factors and genes that modulate important physiological processes. Chemicals are an important component of the environment. Conditions such as asthma, cancer, diabetes, hypertension, immunodeficiency, and Parkinson's disease are known to be influenced by the environment; however, the molecular mechanisms underlying these correlations are not well understood. CTD may help resolve these mechanisms. The most up-to-date extensive list of peer-reviewed scientific articles about CTD is available at their publications page[5]

Core data

CTD is a unique resource where biocurators[6][7] read the scientific literature and manually curate four types of core data:

  • Chemical-gene interactions
  • Chemical-disease associations
  • Gene-disease associations
  • Chemical-phenotype associations

Data integration

By integrating the above four data sets, CTD automatically constructs putative chemical-gene-phenotype-disease networks to illuminate molecular mechanisms underlying environmentally-influenced diseases.

These inferred relationships are statistically scored and ranked and can be used by scientists and computational biologists to generate and verify testable hypotheses about toxicogenomic mechanisms and how they relate to human health.

Users can search CTD to explore scientific data for chemicals, genes, diseases, or interactions between any of these three concepts. Currently,Πρότυπο:When CTD integrates toxicogenomic data for vertebrates and invertebrates.

CTD integrates data from or hyperlinks to these databases:

References

  1. ↑ «The Comparative Toxicogenomics Database (CTD): A Resource for Comparative Toxicological Studies». Journal of Experimental Zoology Part A: Comparative Experimental Biology 305 (9): 689–92. Sep 2006. doi:10.1002/jez.a.307. PMID 16902965. 
  2. ↑ «The Comparative Toxicogenomics Database (CTD): A Cross-Species Resource for Building Chemical-Gene Interaction Networks». Toxicol. Sci. 92 (2): 587–95. Aug 2006. doi:10.1093/toxsci/kfl008. PMID 16675512. 
  3. ↑ «Promoting comparative molecular studies in environmental health research: an overview of the comparative toxicogenomics database (CTD)». Pharmacogenomics J. 4 (1): 5–8. 2004. doi:10.1038/sj.tpj.6500225. PMID 14735110. 
  4. ↑ «The Comparative Toxicogenomics Database (CTD)». Environ. Health Perspect. 111 (6): 793–5. May 2003. doi:10.1289/ehp.6028. PMID 12760826. PMC 1241500. Αρχειοθετήθηκε από το πρωτότυπο στις 2010-06-06. https://web.archive.org/web/20100606135634/http://ehp.niehs.nih.gov/txg/docs/2003/6028/abstract.html. 
  5. ↑ CTD Publications page ctdbase.org
  6. ↑ «Biocurators: Contributors to the World of Science». PLOS Comput. Biol. 2 (10): e142. Oct 2006. doi:10.1371/journal.pcbi.0020142. PMID 17411327. Bibcode: 2006PLSCB...2..142B. 
  7. ↑ «The Biocurator: Connecting and Enhancing Scientific Data». PLOS Comput. Biol. 2 (10): e125. Oct 2006. doi:10.1371/journal.pcbi.0020125. PMID 17069454. Bibcode: 2006PLSCB...2..125S. 
  8. ↑ ChemIDplus US National Library of Medicine, n.d.,retrieved 7 November 2015
  9. ↑ diXa Data Warehouse n.d., retrieved 7 November 2015
  10. ↑ Hendrickx, D. M.; Aerts, H. J. W. L.; Caiment, F.; Clark, D.; Ebbels, T. M. D.; Evelo, C. T.; Gmuender, H.; Hebels, D. G. A. J. και άλλοι. (12 December 2014). «diXa: a data infrastructure for chemical safety assessment». Bioinformatics 31 (9): 1505–1507. doi:10.1093/bioinformatics/btu827. PMID 25505093. 
  11. ↑ Train online, Disease data European Molecular Biology Laboratory,n.d.,retrieved 7 November 2015
  12. ↑ NCBI Taxonomy

External links

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