Constructing ontology-driven protein family databases - Bioinformatics
domain-specific resources based on the same template structure. The formal structure ... tional differences between the two protein families, the ontology model was equally applicable to .... Building protein family resources. The GO describes ...
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UniProt-DAAC: domain architecture alignment and - Bioinformatics
Jun 26, 2016 ... Ontology (GO) project provides the most comprehensive functional ... These are the structural building ... annotations to the domains and families, and approach a protein se- quence as a functional combination of its domains. Some of the widely used sequence-based domain/family databases are Pfam.
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Framework for a Protein Ontology - PIR - Georgetown University
Nov 10, 2006 ... and protein evolutionary families (ontology for protein evolution), to delineate the .... One complication is that domains within a multi-domain protein can be lost in one ... Homology can be asserted for proteins in the same family based ... forms of a given gene product are critical to making precise annotation.
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dcGO: database of domain-centric ontologies on functions
Nov 17, 2012 ... logical terms and protein domains at the superfam- ily and family levels. Some functional ... into families, which often share a higher sequence ... Our domain- centric ontology derived from proteins ... rithm that is used to build it.
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Domains Predicting Gene Ontology Functions from ProDom and
Mar 28, 2006 ... or not a protein has a domain using sequence similarity. As part of the ... method takes advantage of the structure of the GO ontology to make .... to a ProDom domain describing that family. ..... associations considered when building rules. ..... Increased coverage of protein families with the blocks database.
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SUPERFAMILY 1.75 including a domain-centric gene ontology
Nov 9, 2010 ... user to highlight a chosen superfamily, family or domain ... provides the prediction of protein domains of known structure in amino ... contains domain- based gene ontology annotation (GOA) .... We also identified all coiled coil containing families and .... or family. The pipeline of building domain-centric GOAs.
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Protein family classification and functional annotation
iProClass, an integrated database of protein family, function, and structure ... annotation and making annotation errors apparent; (3) ... mixtures of domain families and families of whole ..... of proteins, to develop an ontology of protein names,.
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Evolutionarily consistent families in SCOP: sequence, structure and
We show that SCOP family groupings are evolutionarily consistent to a very high degree ... Protein domains in this context can be regarded as the building blocks of ... A domain can be defined as a protein unit which is seen in nature either on its ... functional labels (in the forms of Gene Ontology and Enzyme Classification).
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A Library of Protein Families and Subfamilies Indexed
PANTHER/X ontology to give a high-level representation of gene function across the human and mouse ... group of related sequences is used to build a statistical represen- ... protein domains). ... Family and domain databases such as Pfam and SMART have ... tion of subfamilies as subtrees of a family tree built from protein.
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SynDB: a Synapse protein DataBase based on synapse ontology
Nov 10, 2006 ... domain families, species, chromosomal locations or Tribe-MCL .... 'Protein Domains' were grouped into InterPro domain family groups which ...
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the domain of biology, where an OWL ontology and an OWL classification tool called the ... protein families, and to data from any sequenced genome—in fact we believe that similar .... family. If a protein contains one of these diagnostic p- domains, it must belong .... 6 We used Protégé 3.0 with OWL plugin 1.3, build 225.1.
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PANTHER: A Library of Protein Families and Subfamilies Indexed by
PANTHER/X ontology to give a high-level representation of gene function across the ... group of related sequences is used to build a statistical represen- ... protein domains). ... Family and domain databases such as Pfam and SMART have.
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dcGOR: An R Package for Analysing Ontologies and Protein - Plos
Oct 30, 2014 ... and protein domain annotations, particularly those in the dcGO ... ontologies and annotations on domains (taken from SCOP, Pfam ... annotate both SCOP domain superfamilies and families . ... Functions for customised data building ..... in 2011: new developments in the family and domain prediction ...
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Protein function prediction using domain families
Feb 28, 2013 ... teins (i.e., single domains or domain combinations) that ... Gene Ontology (GO) [ 20] protein function annotation data (similar ... A protein family resource would build one model per protein family (middle; coloured squares) and.
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Update on genome completion and annotations: Protein Information
proteins function in making up a living cell. The Protein ... integrated database of protein family, function and structure.3. iProClass ... interaction, modification, structure, genome, ontology, literature ... 145,340 families, 5,720 Pfam and PIR homology domains, ... Domain-based or structural classification-based searches allow.
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classification, we resorted to Gene Ontology and domain-architecture based ... relationships among different protein kinase sub-families and also classified ... such associations.12 Often, few domains diverge from this pool ... making them specialized.2,12,17 ... of protein kinases, where sub-family classification is well.
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Protocols to Capture the Functional Plasticity of Protein Domain
Most proteins comprise several domains, segments that are clearly discernable in protein structure and ... Ontology protein function annotations and a set of rules and concepts to derive families is a novel approach to large-scale domain sequence ... building as 'the IT guys', were of great help on several occasions. If I was ...
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D2.5.4 Analysis of Requirements for Further - Knowledge Web
Keyword list: description logics, ontology language, query language, RDF, OWL DL, OWL-E ... Kilburn Building, Department of Computer ..... tools which provide both a component for representing domain knowledge in the form of ..... membership in a particular protein family, i.e., some p-domains only occur in a single.
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Topology based identification and comprehensive - DiVA
genome and assess the 4TM structure group as a whole. .... GO terms, Pfam domain descriptions, and protein family ... Mendelian Inheritance in Man (OMIM) database; the Functional Disease Ontology (FunDO) .... protein families, and the number of proteins identified as drug targets and the drug indications are presented.
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Data Pushing: A Fly-Centric Guide to Bioinformatics Tools
Jan 22, 2008 ... GO, Gene Ontology; iHOP, information Hyperlinked Over Proteins; KEGG, ... PDB, Proteins Data Bank; PFAAT, Protein Family Alignment Annotation Tool ; Pfam, Protein ... Information Resource; ProDom, Protein Domain families database; PSI ... sites, transposon insertions, peptides and protein domains.
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