About neXtProt #

neXtProt은 SIB(Swiss Institute of Bioinformatics)에서 개발한 human에 특화된 protein knowledgebase 데이터베이스이다. 넓은 human analysis에 필요한 protein의 완벽한 정보를 curation을 통해 통합했다. UniProt을 비롯한 15개의 데이터베이스를 담고있다. (3.0.28 release 2015.01.11)

• UniProtKB/Swiss-Prot (UniProt knowledgebase Swiss-Prot section, 2015_12, 2015-08-20)
• BGee (Database for gene expression evolution, 12, 2012-12-20)
• COSMIC (Catalogue of somatic mutations in cancer, 73, 2015-08-28)
• Ensembl (Ensembl human genome browser, 82, 2015-11-20)
• ENZYME (Enzyme nomenclature database, 2015-12-09, 2015-11-19)
• GO (Gene Ontology, 2015-11-17, 2015-11-19)
• HPA (Human Protein Atlas, 13.0, 2015-03-19)
• IntAct (Molecular interaction database, 2015-06-27, 2015-08-26)
• InterPro (Integrated resource of protein families and domains and functional sites, 53.0, 2015-11-25)
• MeSH (Medical Subject Headings, desc2016/2015-11-19, 2015-11-19)
• PeptideAtlas (Peptides identified by mass spectrometry, 201503, 2015-12-15)
• PROSITE (Protein domain and family database, 20.120, 2015-11-25)
• PubMed (Citations for biomedical literature from MEDLINE, life science journals, and online books., 2015-12-07, 2015-12-07)
• SRMAtlas (Targeted proteomics assays, 201408, 2014-08-30)
• UniProt-GOA (Gene Ontology annotations, 2015-11-09, 2015-11-25)

Data classification and searching method #

데이터의 정확성은 금은동으로 나누어 curation했다. 현재는 restrict to gold 검색법과 include silver기능을 제공하고 있으며, 검색방법은 google-like 방식으로 full text input을 적용했다. 예를들어, "find all proteins located in the mitochondrion and expressed in liver" 라고 검색하면 원하는 탐색이 가능하다.

Data statistics #

현재 (3.0.28 release 2016.01.11)까지 neXtProt이 담고 있는 데이터베이스는 아래와 같다.

• Protein entries : 20,055
• Controlled vocabularies : 163,375
• Publications : 476,366

Reference #

• http://www.nextprot.org