The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nature Genetics, 25(1):25--29, 2000.  Home/Search Document Not in Database Summary Related Articles Check |
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Functional Discrimination of Gene Expression Patterns in Terms of.. - Badea (Correct)
....annotations are in free text and thus of little use to an automated analysis program. Despite this, significant efforts are under way to develop a unifying language in terms of which to describe functions of genes, proteins, biological processes and cellular locations. The Gene Ontology (GO) [3] is a large, constantly growing hierarchy of molecular biology concepts, which can be used to annotate genes and proteins with functional information. Such annotations are currently available, e.g. in the Proteome HumanPSD database [4] In this paper, we use Inductive Logic Programming (ILP) 9] ....
....others, Gene Ontology annotations of a large number of human genes (we could find in Proteome 459 of the 918 cDNA clones of Garber et al. Functional annotations are however of little use without some sort of background knowledge that relates the various concepts involved. The Gene Ontology (GO) [3] is a hierarchy of concepts used in molecular biology and genetics, which can be employed as background knowledge for an inductive learner. The ontology is organized according to Molecular Function , Biological Process and Cellular Component , for which we have annotations in the Proteome ....
Gene Ontology Consortium. Gene Ontology: tool for the unification of biology. Nature Genet. 25:25-29, 2000.
Building ontologies in DAML+ OIL - Stevens, al. (2003) (Correct)
....and distributed bioinformatics resources. MyGrid [3] which currently uses an ontology of bioinformatics services to discover, compose and semantically describe services available on the web. The Gene Ontology Next Generation (GONG) 4] which uses a DL to migrate the Gene Ontology (GO)[5] to an explicitly defined form that delivers a more complete and robust ontology. Running through all these projects is the theme of DLs as a knowledge representation language. In this article we argue why we think this particular representation is good for describing biomedical knowledge and why ....
....the provision of a medical service or procedure. Similarly, bioinformatics has seen the need for controlled vocabularies, such as the SWISS PROT keywords (http: www.expasy.ch cgi bin keywlist.pl) 8] to index its database entries and ease retrieval. Recent activities in bioinformatics, such as GO [5], have seen the use of ontologies as a means of delivering controlled vocabularies. Traditionally, in these terminologies each concept or term has been placed by hand within the classification. Experience has shown that this approach, while an easy and attractive method to start with, is fraught ....
The Gene Ontology Consortium. 2000. Gene Ontology: tool for the unification of biology. Nature Genet 25: 25 -- 29.
Medical Informatics: Searching for Underlying Components - Musen (Correct)
....are central to much current work in bioinformatics. At the same time, now that most of the genome is known, the bioinformatics community recognizes the importance of building ontologies that can help to structure this information and to relate specific genes to their physiological function [26]. Informatics as an Academic Discipline At Stanford, we now teach the course that introduces first year graduate students to the principles of biomedical informatics in terms of the development and application of domain ontologies and problem solving methods [27] The course begins with a ....
The gene ontology consortium. Gene ontology: tool for the unification of biology. Nature Genetics. 1:25--29, 2000.
Managing Biological Information Using Biological Knowledge - Goble, Stevens (Correct)
....in query refinements, as users can move within the ontology to specialise or generalise query terms used. Such controlled vocabularies also enhance recall and precision all of the data items for a given term are retrieved, but only data with those terms are retrieved. The Gene Ontology (GO) [17] is an example of this approach. The Schulze Kremer ontology for molecular biology (MBO) 14] has a related purpose, offering a community wide description of domain knowledge, giving a shared understanding of differing conceptualisations used across resources. ii Ontologies are also used to ....
The Gene Ontology Consortium. Gene Ontology: Tool for the Unification of Biology. Nature Genetics, 25:25--29, 2000.
Agent Interaction for Bioinformatics Data Management - Bryson, Luck, Joy, Jones (2002) (3 citations) (Correct)
....agent. unregister Cancels a register (and any commitments of the agent) Table 3: Description of BAL performatives. wide range of languages to represent data and data queries, including SQL, XML, XQL and ASN1 [1] and several ontologies are being developed for use within different sub fields [7, 13]. Currently, however, we employ a simple content language and simple ontologies, although it is clearly beneficial to permit different languages and ontologies to be used within specialized sub communities of agents. The page count is used, for example, when a long list of data items which cannot ....
....(page=0) send: tell (page 0) Figure 7: State transition diagram for the do, derive and query interaction protocols. The Error and Timeout states are not shown for clarity. that need to be considered (for example in relation to the potential use of different data languages [1] and ontologies [7, 13] to provide a consistent language for the description of biological data) but these are separate concerns and we do not consider them further here. It should be clear though that since the BAL interaction language is at a higher level it permits different underlying content languages to be ....
THE GENE ONTOLOGY CONSORTIUM. Gene Ontology: tool for the unification of biology. Nature Genetics, 25:25--29, 2000.
OILing the way to Machine Understandable.. - Stevens, Goble.. (2001) (Correct)
....There have been several attempts to develop bioinformatics ontologies to exploit biological information. Ontologies are used as repositories of potentially reusable biological knowledge, as a common framework for multi database queries [4] or as controlled vocabularies for genome annotation [21]. The success of many biological databases depends upon their fidelity to, and the clear communication of, their ontologies to prevent errors of data entry and interpretation. The Gene Ontology (GO) 21] is a controlled vocabulary for annotating a gene product s for molecular functions, the ....
....framework for multi database queries [4] or as controlled vocabularies for genome annotation [21] The success of many biological databases depends upon their fidelity to, and the clear communication of, their ontologies to prevent errors of data entry and interpretation. The Gene Ontology (GO) [21] is a controlled vocabulary for annotating a gene product s for molecular functions, the biological processes in which it is involved and the cellular locations in which it is found. GO takes the form of phrases organised into a hierarchical classification. EcoCyc [17] has used an ontology to ....
The Gene Ontology Consortium. Gene Ontology: Tool for the Unification of Biology. Nature Genetics, 25:25--29, 2000. 10
An Algebra for Semantic Interoperability of Information Sources - Mitra, Wiederhold (2001) (3 citations) (Correct)
....Base of Databases(KoD) Correspondingly, we assume that associated with each information source is an ontology. However, we do not require all ontologies to be saved in a central repository like the KoD. In the recent years, several ontologies have been developed in the biological sciences e.g. [6] (for a comprehensive list see [7] The ontologies associated with information sources are based on some existing, known vocabularies and conceptual models. Native drivers and wrappers provide access to the ontologies and help us restructure the information if needed. We establish ....
The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nature Genetics, 25:25-- 29, 2000.
Journal of Machine Learning Research 7 (2006).. - Parsimonious.. Self-citation (Genetics) (Correct)
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The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nature Genetics, 25(1):25--29, 2000.
Inter-Element Dependency Models for Sequence Classification - Silvescu, Andorf, Dobbs.. (2004) Self-citation (Biology) (Correct)
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The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nature Genet., (25):25--29, 2000.
Knowledge acquisition, consistency checking and.. - Yeh, Karp, Noy, Altman (2003) Self-citation (Ontology) (Correct)
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The Gene Ontology Consortium (2000) Gene ontology: tool for the unification of biology. Nature Genet., 25, 25--29.
The Drug Ontology Project for Elsevier - An RDF.. - Broekstra, Fluit, .. (2004) Self-citation (Ontology) (Correct)
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The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nature Genetics, 25(1):25--29, May 2000.
The Drug Ontology Project for Elsevier - An RDF.. - Broekstra, Fluit, .. Self-citation (Ontology) (Correct)
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The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nature Genetics, 25(1):25--29, May 2000.
Navigating towards Biologically Resolved Diagnoses .. - Lottaz, Floch.. (2003) Self-citation (Biology) (Correct)
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The Gene Ontology Consortium. Gene ontology: Tool for the unification of biology. Nature Genetics, 25:25--29, May 2000.
Goat: The Gene Ontology Annotation Tool - Michael Bada Robin (2003) Self-citation (Ontology) (Correct)
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The Gene Ontology Consortium (2000). Gene Ontology: tool for the unification of biology. Nature Genetics, 25: 25-29.
Identification Of Human Transcription Factor.. - Caselle.. (2003) Self-citation (Genetics) (Correct)
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The Gene Ontology Consortium (2000) "Gene Ontology: tool for the unification of biology." Nature Genetics 25:25,29.
Computational Identification of Transcription Factor.. - Functional Analysis Of (2003) Self-citation (Ontology) (Correct)
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The Gene Ontology Consortium (2000) "Gene Ontology: tool for the unification of biology." Nature Genetics 25:25,29.
The Ontology of the Gene Ontology - Smith, Williams, Schulze-Kremer (2003) (3 citations) Self-citation (Ontology) (Correct)
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The Gene Ontology Consortium. Gene Ontology: tool for the unification of biology. Nature Genet. 2000; 25: 25-29.
The Unified Medical Language System and the Gene Ontology.. - Kumar, Smith (2003) Self-citation (Ontology) (Correct)
....vocabulary for the description of genes and gene products. Currently, efforts are underway to imcorporate GO into UMLS. GO s compilers have endeavored to develop a standardized cross species biological vocabulary that can be used by multiple databases to annotate them in a consistent way [3,4,5]. As of June 2003, GO takes the form of a list of some 14,000 common biological terms together with text intended to convey definitions of many of the terms listed. Terms are organized in parent child hierarchies, indicating that one term is more general than another. Additional information is ....
The Gene Ontology Consortium. Gene Ontology: tool for the unification of biology. Nature Genet. 2000; 25: 25-29
Gene Ontology-Facilitated Genome Analysis - Xie (2003) Self-citation (Ontology) (Correct)
....cluster, antisense genes, microarray analysis. GENE ONTOLOGY AND GENE ONTOLOGY ANNOTATION Biomedical knowledge is encapsulated in tens of millions of publications with various degrees of coherence and computability. Such unstructured form is regarded as an obstacle in research and development [1]. Gene Ontology (GO) has been developed to facilitate the knowledge representation and efficient biomedical information management [1 4] and has been widely incorporated into academic and industrial knowledge databases [for example, 5 8] Almost all recent publications on large scale genome ....
....tens of millions of publications with various degrees of coherence and computability. Such unstructured form is regarded as an obstacle in research and development [1] Gene Ontology (GO) has been developed to facilitate the knowledge representation and efficient biomedical information management [1 4] and has been widely incorporated into academic and industrial knowledge databases [for example, 5 8] Almost all recent publications on large scale genome projects, such as those discussing genome sequencing and analysis for Drosophila, human, mouse and other organisms utilized GO for gene ....
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The Gene Ontology Consortium. Gene Ontology: tool for the unification of biology. Nat. Genet., 2000, 25: 25-29.
The Lexical Properties of the Gene Ontology (GO) - McCray, Browne, Bodenreider (2002) Self-citation (Consortium) (Correct)
....pathologies, etc. though there are some exceptions. The concepts needed at the molecular level are beginning to be represented by efforts such as the Gene Ontology (GO) initiative. GO is a construct developed for the purpose of annotating molecular information about genes and their products. [3 5]. The ontology is a shared resource developed by the GO Consortium, a group of scientists who work on a variety of model organisms. The developers are interested in creating a resource that will allow for interoperability among genomic databases and that can be used irrespective of the particular ....
Gene Ontology Consortium. Gene Ontology: tool for the unification of biology. Nature Genetics 2000 May; 25:25-9.
Gene Ontology Driven Classification of Gene Expression.. - Lottaz, Bentink, Spang Self-citation (Ontology) (Correct)
....conjecture that the mentioned problems can be tackled by giving the classifier a biologically meaningful structure, i.e. by dividing the classification task into subtasks according to biological criteria. Structuring biological knowledge is one of the central goals of the Gene Ontology database [2]. Biological terms related to molecular functions, biological processes and cellular components are collected into a directed acyclic graph where each node represents a term and child terms are either members or representatives of their parent terms. Moreover, genes are attributed to GO nodes ....
The Gene Ontology Consortium. Gene ontology: Tool for the unification of biology. Nature Genetics, 25:25--29, May 2000.
Ontology Development for a Pharmacogenetics Knowledge.. - Oliver, Rubin, Stuart.. (2001) (3 citations) Self-citation (Ontology) (Correct)
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The Gene Ontology Consortium, "Gene ontology: tool for the unification of biology" Nature Genetics 25, 25-9 (2000)
Ontology Development For A Pharmacogenetics Knowledge.. - Oliver, Rubin, Stuart.. (2002) (3 citations) Self-citation (Ontology) (Correct)
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The Gene Ontology Consortium, "Gene ontology: tool for the unification of biology" Nature Genetics 25, 25-9 (2000)
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The Gene Ontology Consortium (2000). Gene Ontology: Tool for the unification of biology. Nature Genetics, 25, 25--29.
Modelling biological processes using workflow and Petri Net.. - Peleg, Yeh, Altman (2002) (1 citation) (Correct)
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The Gene Ontology Consortium, (2000) Gene Ontology: tool for the unification of biology. Nature Genet., 25,25--29.
Structure-Based Partitioning of Large Concept Hierarchies - Stuckenschmidt, Klein (2004) (Correct)
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The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nature Genetics, 25:25--29, 2000.
Structure-Based Partitioning of Large Concept Hierarchies - Stuckenschmidt, Klein (Correct)
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The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nature Genetics, 25:25--29, 2000.
Merging DAML+OIL bio-ontologies - Anna (Correct)
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The Gene Ontology Consortium. Gene Ontology: tool for the unification of biology. Nature Genetics, 25:25-29, 2000. http://www.geneontology.org/
An Ontology-Driven Querying Environment for Biological .. - Kroth, Pinto.. (2003) (Correct)
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Gene Ontology Consortium. Gene Ontology: tool for the unification of biology. Nature Genetics, vol.25, 2000, 25-29.
GENKOMB project report - Jakub Orzechowski Westholm (2003) (Correct)
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The Gene Ontology Consortium. Gene Ontology: tool for the unification of biology. Nature Genetics 25: 25-29. 2000 39
Reconstruction of Intercellular Communication Networks - Skusa, Prank, Köhler (2003) (Correct)
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The Gene Ontology Consortium, Gene Ontology: tool for the unification of biology, Nature Genetics 25: 25-29, 2000.
Towards Automatic Partitioning of Class Hierarchies - Stuckenschmidt, Klein (Correct)
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The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nature Genetics, 25:25-- 29, 2000.
Poset Ontologies and Concept Lattices as Semantic Hierarchies - Joslyn (Correct)
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Gene Ontology Consortium: (2000) "Gene Ontology: Tool For the Unification of Biology", Nature Genetics,v.25:1, pp. 25-29
Identifying Underlying Factors in Breast Cancer.. - Berger.. (2003) (Correct)
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The Gene Ontology Consortium, "Gene Ontology: Tool for the Unification of Biology," Nature Genetics, vol. 25, no. 1, pp. 25--29, May 2000.
The Utility of Different Representations of Protein.. - King, Karwath, Clare, .. (2000) (1 citation) (Correct)
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TB gene list, http://www.sanger.ac.uk/Projects/M tuberculosis/ Gene List/. The Gene Ontology Consortium, (2000) Gene ontology: tool for the unification of biology. Nature Genet., 25,25--29.
The Utility of Different Representations of Protein.. - King, Karwath, Clare, .. (2001) (1 citation) (Correct)
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The Gene Ontology Consortium (2000) Gene Ontology: tool for the unification of biology. Nature Genet. 25, 25-29 21
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