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GOAnnotator: linking protein GO annotations to evidence text

Francisco M Couto, Mário J Silva, Vivian Lee, Emily Dimmer, Evelyn Camon, Rolf Apweiler, Harald Kirsch, Dietrich Rebholz-Schuhmann
2006 Journal of Biomedical Discovery and Collaboration  
Therefore, instead of curated annotations most of the proteins come with uncurated annotations, which have been generated automatically.  ...  The selection of the text is based on the similarity of the text to the term from the uncurated annotation.  ...  This work was supported by the Marie Curie Training Sites scheme of the European Commission's Quality of Life Programme (Contract no. QLRI-1999-50595).  ... 
doi:10.1186/1747-5333-1-19 pmid:17181854 pmcid:PMC1769513 fatcat:achxzgkicfei5d7tdiz73retvm

PASS: Protein Annotation Surveillance Site for Protein Annotation Using Homologous Clusters, NLP, and Sequence Similarity Networks

Jin Tao, Kelly A. Brayton, Shira L. Broschat
2021 Frontiers in Bioinformatics  
At the same time, computational analysis is widely used for protein annotation, but a dearth of experimental verification has contributed to inaccurate annotation as well as to annotation error propagation  ...  Thus, a tool to help life scientists with accurate protein annotation would be useful.  ...  Lack of experimental verification contributes to inaccurate protein annotation and the propagation of existing annotation errors.  ... 
doi:10.3389/fbinf.2021.749008 fatcat:64pixdq3rfeq3pm4qv7bei3hjy

Automated Confirmation of Protein Annotation Using NLP and the UniProtKB Database

Jin Tao, Kelly A. Brayton, Shira L. Broschat
2020 Applied Sciences  
Many protein sequences are annotated using computational analysis rather than experimental verification, leading to inaccuracies in annotation.  ...  In this work we present a novel approach for automatically confirming the existence of manually curated information with experimental evidence of protein annotation.  ...  validation, the majority of which are in the uncurated UniProtKB/TrEMBL database.  ... 
doi:10.3390/app11010024 fatcat:o7tbtpwbdbbetf72b55dtl4y2u

Integrating protein-protein interactions and text mining for protein function prediction

Samira Jaeger, Sylvain Gaudan, Ulf Leser, Dietrich Rebholz-Schuhmann
2008 BMC Bioinformatics  
Functional annotation of proteins remains a challenging task.  ...  For a subset of proteins we predicted new GO annotations that were not available in UniProtKb/Swiss-Prot.  ...  Acknowledgements This research work has been supported by the Network of Excellence 'Semantic Interoperability and Data Mining in Biomedicine' (NoE 507505).  ... 
doi:10.1186/1471-2105-9-s8-s2 pmid:18673526 pmcid:PMC2500093 fatcat:qiw5bnhdgfagllyteckwlqdcim

The carbohydrate-active enzyme database: functions and literature

Elodie Drula, Marie-Line Garron, Suzan Dogan, Vincent Lombard, Bernard Henrissat, Nicolas Terrapon
2021 Nucleic Acids Research  
The three primary tasks of the CAZy curators are (i) to maintain and update the family classification of this class of enzymes, (ii) to classify sequences newly released by GenBank and the Protein Data  ...  We present several important changes that facilitate taxonomic navigation, and allow to download the entirety of the annotations.  ...  Swiss-Prot, the manually curated part of UniProt, is another widely recognized source of functional information for proteins (565k proteins in Swiss-Prot; 219M in uncurated TrEMBL (11, 12) ).  ... 
doi:10.1093/nar/gkab1045 pmid:34850161 pmcid:PMC8728194 fatcat:y23fx6empveure4shj35pa6tka

Evaluating a variety of text-mined features for automatic protein function prediction with GOstruct

Christopher S Funk, Indika Kahanda, Asa Ben-Hur, Karin M Verspoor
2015 Journal of Biomedical Semantics  
One advantage of using literature features is their ability to offer easy verification of automated predictions.  ...  Additionally, we present a "medium-throughput" pipeline that was used to annotate a large subset of co-mentions; we suggest that this strategy could help to speed up the rate at which proteins are curated  ...  through the ICT Centre of Excellence program.  ... 
doi:10.1186/s13326-015-0006-4 pmid:26005564 pmcid:PMC4441003 fatcat:pz7pgludtjgm3ndkcl56ir26am

An integrative approach to ortholog prediction for disease-focused and other functional studies

Yanhui Hu, Ian Flockhart, Arunachalam Vinayagam, Clemens Bergwitz, Bonnie Berger, Norbert Perrimon, Stephanie E Mohr
2011 BMC Bioinformatics  
DIOPT also displays protein and domain alignments, including percent amino acid identity, for predicted ortholog pairs.  ...  the functions of orthologs in other species.  ...  Acknowledgements and Funding The authors would like to thank members of the Perrimon lab and Lizabeth Perkins for helpful suggestions and discussions.  ... 
doi:10.1186/1471-2105-12-357 pmid:21880147 pmcid:PMC3179972 fatcat:jtvaobinn5dzrgyl4omxu73spi

Biomedical text mining and its applications in cancer research

Fei Zhu, Preecha Patumcharoenpol, Cheng Zhang, Yang Yang, Jonathan Chan, Asawin Meechai, Wanwipa Vongsangnak, Bairong Shen
2013 Journal of Biomedical Informatics  
Cancer is a malignant disease that has caused millions of human deaths. Its study has a long history of well over 100 years. There have been an enormous number of publications on cancer research.  ...  The immense body and rapid growth of biomedical text on cancer has led to the appearance of a large number of text mining techniques aimed at extracting novel knowledge from scientific text.  ...  , constituency (phrase structure) syntactic annotation, term annotation, event annotation, relation annotation, and coreference annotation PICorpus [171, 172] PICorpus is a protein-protein interaction  ... 
doi:10.1016/j.jbi.2012.10.007 pmid:23159498 fatcat:xd7j77sbwfhklkat6tael64lbq

Genome-wide transcriptional changes induced by phagocytosis or growth on bacteria in Dictyostelium

Alessio Sillo, Gareth Bloomfield, Alessandra Balest, Alessandra Balbo, Barbara Pergolizzi, Barbara Peracino, Jason Skelton, Alasdair Ivens, Salvatore Bozzaro
2008 BMC Genomics  
A few putative receptors, including GPCR family 3 proteins, scaffolding and adhesion proteins, components of signal transduction and transcription factors have been identified, which could be part of a  ...  Functional annotation of differentially regulated genes with different tools revealed that phagocytosis induces profound changes in carbohydrate, aminoacid and lipid metabolism, and in cytoskeletal components  ...  This work was supported by funds of the Italian Ministry of University (PRIN'04), the Piedmont Region (Ricerca Sanitaria) and University of Turin to SB and Wellcome Trust grant 06724 to AI.  ... 
doi:10.1186/1471-2164-9-291 pmid:18559084 pmcid:PMC2443395 fatcat:7rzxzbyu4jbp5cpog4zuxplbjm

Quality of Computationally Inferred Gene Ontology Annotations

Nives Škunca, Adrian Altenhoff, Christophe Dessimoz, Lars Juhl Jensen
2012 PLoS Computational Biology  
Gene Ontology (GO) has established itself as the undisputed standard for protein function annotation.  ...  By exploiting changes in successive releases of the UniProt Gene Ontology Annotation database, we assessed the quality of electronic annotations in terms of specificity, reliability, and coverage.  ...  Uncurated-electronic-annotations are generally considered to be least reliable.  ... 
doi:10.1371/journal.pcbi.1002533 pmid:22693439 pmcid:PMC3364937 fatcat:qsmzh6dcxrht3ns5eyliupxf4u

The Xenopus ORFeome: A resource that enables functional genomics

Ian M. Grant, Dawit Balcha, Tong Hao, Yun Shen, Prasad Trivedi, Ilya Patrushev, Joshua D. Fortriede, John B. Karpinka, Limin Liu, Aaron M. Zorn, P. Todd Stukenberg, David E. Hill (+1 others)
2015 Developmental Biology  
Transfer into the Gateway system was validated by 5′ and 3′ end sequencing of the entire collection and protein expression of a set of test clones.  ...  Functional characterisation of proteins and large-scale, systems-level studies are enabled by extensive sets of cloned open reading frames (ORFs) in an easily-accessible format that enables many different  ...  Fifteen of these gave immunoblot products of the expected molecular weight (Fig. 1e) . Given the sequence verification, it is unclear why the other two proteins were not correctly translated.  ... 
doi:10.1016/j.ydbio.2015.09.004 pmid:26391338 pmcid:PMC4684507 fatcat:tvqgwdoiazbprfwygj6ncsi6zu

Expansion of the Protein Repertoire in Newly Explored Environments: Human Gut Microbiome Specific Protein Families

Kyle Ellrott, Lukasz Jaroszewski, Weizhong Li, John C. Wooley, Adam Godzik, David T. Jones
2010 PLoS Computational Biology  
Using an automated procedure, we identified a group of protein families strongly overrepresented in the human gut.  ...  To identify other protein families that are specific to this environment, we investigated the distribution of protein families in the currently available human gut genomic and metagenomic data.  ...  Acknowledgments We would like to acknowledge all our colleagues from the JCSG, as well as from other PSI structural genomics centers, for continuous discussions and comments during the preliminary stage of  ... 
doi:10.1371/journal.pcbi.1000798 pmid:20532204 pmcid:PMC2880560 fatcat:dzt6ycbrkjambgrt4v43jb7b6u

Integrated Bioinformatics Analysis Reveals Marker Genes and Potential Therapeutic Targets for Pulmonary Arterial Hypertension

Aoqi Li, Jin He, Zhe Zhang, Sibo Jiang, Yun Gao, Yuchun Pan, Huanan Wang, Lenan Zhuang
2021 Genes  
Our research analyzed three microarray datasets of lung tissues from human PAH samples retrieved from the Gene Expression Omnibus (GEO) database.  ...  Two of them (CDC5L and DDX46) were found to be significantly upregulated both in the merged dataset and the validating dataset in PAH patients.  ...  Acknowledgments: Several experiments were done under the kind help from Yulan Jin of The Experimental Teaching Center, College of Animal Sciences, Zhejiang University.  ... 
doi:10.3390/genes12091339 pmid:34573320 pmcid:PMC8467453 fatcat:xj3z2zb7mja55c5r733lta5d64

The bovine lactation genome: insights into the evolution of mammalian milk

Danielle G Lemay, David J Lynn, William F Martin, Margaret C Neville, Theresa M Casey, Gonzalo Rincon, Evgenia V Kriventseva, Wesley C Barris, Angie S Hinrichs, Adrian J Molenaar, Katherine S Pollard, Nauman J Maqbool (+7 others)
2009 Genome Biology  
The most divergent proteins in milk were associated with nutritional and immunological components of milk, whereas highly conserved proteins were associated with secretory processes.  ...  Consensus tree construction Single copy ortholog identifiers of milk protein genes were extracted from the whole genome set of orthologous clusters (see 'Orthology delineation' in Materials and methods  ...  For each major trend shown in Figure 3 , rates of occurrence among the uncurated orthologs of the milk protein and lactation mammary gene sets were compared with the orthologs of all bovine consensus  ... 
doi:10.1186/gb-2009-10-4-r43 pmid:19393040 pmcid:PMC2688934 fatcat:6m34jc3wbjhqjj7ywznlbkbjym

Computationally Driven, Quantitative Experiments Discover Genes Required for Mitochondrial Biogenesis

David C. Hess, Chad L. Myers, Curtis Huttenhower, Matthew A. Hibbs, Alicia P. Hayes, Jadine Paw, John J. Clore, Rosa M. Mendoza, Bryan San Luis, Corey Nislow, Guri Giaever, Michael Costanzo (+3 others)
2009 PLoS Genetics  
Nearly half of these newly characterized proteins are conserved in mammals, including several orthologs known to be involved in human disease.  ...  protein required for normal mitochondrial motility.  ...  Acknowledgments We thank Charlie Boone for reagents and technical assistance, David Botstein for the suggested use of tetrazolium in our petite assays, and Erica Pang for the integrated mitochondrial GFP  ... 
doi:10.1371/journal.pgen.1000407 pmid:19300474 pmcid:PMC2648979 fatcat:ipjbwrbp5rdrbmnmodnibdwgxa
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