Results 21 to 30 of about 463,290 (301)

Mining the Gene Wiki for functional genomic knowledge

BMC Genomics, 2011
Background Ontology-based gene annotations are important tools for organizing and analyzing genome-scale biological data. Collecting these annotations is a valuable but costly endeavor.
Good Benjamin M, Howe Douglas G, Lin Simon M, Kibbe Warren A, Su Andrew I   +4 more
doaj   +1 more source

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report.

PLoS Computational Biology, 2012
A recent paper (Nehrt et al., PLoS Comput. Biol. 7:e1002073, 2011) has proposed a metric for the "functional similarity" between two genes that uses only the Gene Ontology (GO) annotations directly derived from published experimental results.
Paul D Thomas, Valerie Wood, Christopher J Mungall, Suzanna E Lewis, Judith A Blake, Gene Ontology Consortium   +5 more
doaj   +1 more source

Wormbase Curation Interfaces and Tools [PDF]

, 2010
Curating biological information from the published literature can be time- and labor-intensive especially without automated tools. WormBase1 has adopted several curation interfaces and tools, most of which were built in-house, to help curators recognize
Xiaodong Wang
core   +2 more sources

Gene Ontology Annotations and Resources [PDF]

Nucleic Acids Research, 2012
The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations.
Gene Ontology Consortium, Blake, JA, Dolan, M, Drabkin, H, Hill, DP, Li, Ni, Sitnikov, D, Bridges, S, Burgess, S, Buza, T, McCarthy, F, Peddinti, D, Pillai, L, Carbon, S, Dietze, H, Ireland, A, Lewis, SE, Mungall, CJ, Gaudet, P, Chrisholm, RL, Fey, P, Kibbe, WA, Basu, S, Siegele, DA, McIntosh, BK, Renfro, DP, Zweifel, AE, Hu, JC, Brown, NH, Tweedie, S, Alam-Faruque, Y, Apweiler, R, Auchinchloss, A, Axelsen, K, Bely, B, Blatter, M-C, Bonilla, C, Bouguerleret, L, Boutet, E, Breuza, L, Bridge, A, Chan, WM, Chavali, G, Coudert, E, Dimmer, E, Estreicher, A, Famiglietti, L, Feuermann, M, Gos, A, Gruaz-Gumowski, N, Hieta, R, Hinz, C, Hulo, C, Huntley, R, James, J, Jungo, F, Keller, G, Laiho, K, Legge, D, Lemercier, P, Lieberherr, D, Magrane, M, Martin, MJ, Masson, P, Mutowo-Muellenet, P, O'Donovan, C, Pedruzzi, I, Pichler, K, Poggioli, D, Porras Millán, P, Poux, S, Rivoire, C, Roechert, B, Sawford, T, Schneider, M, Stutz, A, Sundaram, S, Tognolli, M, Xenarios, I, Foulgar, R, Lomax, J, Roncaglia, P, Khodiyar, VK, Lovering, RC, Talmud, PJ, Chibucos, M, Giglio, M Gwinn, Chang, H-Y, Hunter, S, McAnulla, C, Mitchell, A, Sangrador, A, Stephan, R, Harris, MA, Oliver, SG, Rutherford, K, Wood, V, Bahler, J, Lock, A, Kersey, PJ, McDowall, DM, Staines, DM, Dwinell, M, Shimoyama, M, Laulederkind, S, Hayman, T, Wang, S-J, Petri, V, Lowry, T, D'Eustachio, P, Matthews, L, Balakrishnan, R, Binkley, G, Cherry, JM, Costanzo, MC, Dwight, SS, Engel, SR, Fisk, DG, Hitz, BC, Hong, EL, Karra, K, Miyasato, SR, Nash, RS, Park, J, Skrzypek, MS, Weng, S, Wong, ED, Berardini, TZ, Huala, E, Mi, H, Thomas, PD, Chan, J, Kishore, R, Sternberg, P, Van Auken, K, Howe, D, Westerfield, M   +136 more
openaire   +4 more sources

Functional-network-based gene set analysis using gene-ontology. [PDF]

PLoS ONE, 2013
To account for the functional non-equivalence among a set of genes within a biological pathway when performing gene set analysis, we introduce GOGANPA, a network-based gene set analysis method, which up-weights genes with functions relevant to the gene ...
Billy Chang, Rafal Kustra, Weidong Tian
doaj   +1 more source

Controlled vocabularies in bioinformatics: A case study in the Gene Ontology [PDF]

, 2004
The automatic integration of information resources in the life sciences is one of the most challenging goals facing biomedical informatics today. Controlled vocabularies have played an important role in realizing this goal, by making it possible to draw ...
Anand Kumar, Bada, Barry Smith, Gene Ontology Consortium, Grenon, Hahn, Kumar, Ogren, Schulz, Smith, Smith, Smith   +11 more
core   +1 more source

Construction of ontology augmented networks for protein complex prediction.

PLoS ONE, 2013
Protein complexes are of great importance in understanding the principles of cellular organization and function. The increase in available protein-protein interaction data, gene ontology and other resources make it possible to develop computational ...
Yijia Zhang, Hongfei Lin, Zhihao Yang, Jian Wang   +3 more
doaj   +1 more source

Inferring gene ontologies from pairwise similarity data. [PDF]

, 2014
MotivationWhile the manually curated Gene Ontology (GO) is widely used, inferring a GO directly from -omics data is a compelling new problem. Recognizing that ontologies are a directed acyclic graph (DAG) of terms and hierarchical relations, algorithms ...
Bafna, Vineet, Dutkowski, Janusz, Ideker, Trey, Kramer, Michael, Yu, Michael   +4 more
core   +2 more sources

GoFigure: Automated Gene Ontology™ annotation [PDF]

Bioinformatics, 2003
Abstract Summary: We have developed a web tool to predict Gene Ontology (GO) terms. The tool accepts an input DNA or protein sequence, and uses BLAST to identify homologous sequences in GO annotated databases. A graph is returned to the user via email. Availability: The tool is freely available at: http://udgenome.ags.udel.
Salim, Khan, Gang, Situ, Keith, Decker, Carl J, Schmidt   +3 more
openaire   +2 more sources

Disjunctive shared information between ontology concepts: application to Gene Ontology

Journal of Biomedical Semantics, 2011
Background The large-scale effort in developing, maintaining and making biomedical ontologies available motivates the application of similarity measures to compare ontology concepts or, by extension, the entities described therein.
Couto Francisco M, Silva Mário J
doaj   +1 more source