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PubMed Text Similarity Model and its application to curation efforts in the Conserved Domain Database

2019 Database: The Journal of Biological Databases and Curation  
This study proposes a text similarity model to help biocuration efforts of the Conserved Domain Database (CDD).  ...  articles in the PubMed Central database.  ...  In this manuscript, we first give an overview of the CDD database of curated protein domains, and we discuss text similarity research, its applications and related work.  ... 
doi:10.1093/database/baz064 pmid:31267135 pmcid:PMC6606757 fatcat:hegduu77gjgo3mnw6rnav3so5m

Database resources of the National Center for Biotechnology Information

E. W. Sayers, T. Barrett, D. A. Benson, E. Bolton, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, S. Federhen, M. Feolo, I. M. Fingerman (+30 others)
2010 Nucleic Acids Research  
ABSTRACT In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov) provides analysis and retrieval resources  ...  for the data in GenBank and other biological data made available through the NCBI Web site.  ...  Go to: PubChem PubChem (51,52) DOMAINS AND STRUCTURES Molecular Modeling Database Molecular Modeling Database (MMDB) (53) contains experimentally determined coordinate sets from PDB ) . ) Conserved  ... 
doi:10.1093/nar/gkq1172 pmid:21097890 pmcid:PMC3013733 fatcat:evc3u4jqubchjoqyvc3ff5qple

HUPHO: the human phosphatase portal

S Liberti, A Calderone, F Sacco, L Perfetto, M Iannuccelli, S Panni, E Santonico, A Palma, AP Nardozza, L Castagnoli, G Cesareni
2012 EMBnet journal  
In addition we present a text-mining-assisted annotation effort aimed at extracting phosphatase related data reported in the scientific literature.  ...  Phosphatases and kinases contribute to the regulation of protein phosphorylation homeostasis in the cell.  ...  Acknowledgement This work was supported by Telethon (GGP09243), the Italian Association for Cancer Research (AIRC), the FIRB project Oncodiet and the FP7 projects Affinomics and PSIMEX.  ... 
doi:10.14806/ej.18.a.380 fatcat:gvf4j6ktezcnnaxzvqnzmdbjn4

TFCat: the curated catalog of mouse and human transcription factors

Debra L Fulton, Saravanan Sundararajan, Gwenael Badis, Timothy R Hughes, Wyeth W Wasserman, Jared C Roach, Rob Sladek
2009 Genome Biology  
All data and userfeedback mechanisms are available at the TFCat portal  ...  The collection, including proven and homology-based candidate TFs, is annotated within a function-based taxonomy and DNA-binding proteins are organized within a classification system.  ...  RS is a Chercheur-boursier of the Fonds de la recherche en santé du Québec and receives operating funds from CIHR to support his research.  ... 
doi:10.1186/gb-2009-10-3-r29 pmid:19284633 pmcid:PMC2691000 fatcat:zhim73vpqneangip2a6ufw2bla

Database resources of the National Center for Biotechnology Information

2013 Nucleic Acids Research  
In addition to maintaining the GenBank Õ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other  ...  biological data made available through the NCBI web site.  ...  MOLECULAR STRUCTURE AND PROTEOMICS Databases The in Entrez through the 'Conserved Domains' link.  ... 
doi:10.1093/nar/gkt1146 pmid:24259429 pmcid:PMC3965057 fatcat:otokyran6rhjvhb2wtyt2z6hvu

Database resources of the National Center for Biotechnology Information

Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Evan Bolton, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Scott Federhen, Michael Feolo, Lewis Y. Geer (+28 others)
2009 Nucleic Acids Research  
In addition to maintaining the GenBank Õ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other  ...  biological data made available through the NCBI web site.  ...  The Conserved Domain Architecture Retrieval Tool allows searches of protein databases on the basis of a conserved domain and returns the domain architectures of database proteins containing the query domain  ... 
doi:10.1093/nar/gkp967 pmid:19910364 pmcid:PMC2808881 fatcat:duzfi6ea4rdvvb5wbhr7z2mbpq

Text Mining Improves Prediction of Protein Functional Sites

Karin M. Verspoor, Judith D. Cohn, Komandur E. Ravikumar, Michael E. Wall, Neil R. Smalheiser
2012 PLoS ONE  
The text-based predictions were also substantially supported by the functional site annotations: compared to other residues, residues mentioned in text were roughly six times more likely to be found in  ...  The text mining extracts mentions of residues in the literature, and predicts that residues mentioned are functionally important.  ...  Acknowledgments We gratefully acknowledge Kevin Nagel for sharing the annotated text corpus he developed for his dissertation work with us and giving us permission to redistribute it.  ... 
doi:10.1371/journal.pone.0032171 pmid:22393388 pmcid:PMC3290545 fatcat:4564uparzzb6ldzy2wxjpap2w4

BBP: Brucella genome annotation with literature mining and curation

Zuoshuang Xiang, Wenjie Zheng, Yongqun He
2006 BMC Bioinformatics  
It is partially due to the lack of a literature mining and curation system able to efficiently incorporate the large amount of literature data into genome annotation.  ...  The BBP InterBru database and Brucella Genome Browser allow users to search and analyze genes of 4 currently available Brucella genomes and link to more than 20 existing databases and analysis programs  ...  Acknowledgements WZ was supported by the NIH-NIAID R21 grant (#1R21AI057875-01) to Dr. He. ZX was supported by Dr. He's startup funding from the University of Michigan.  ... 
doi:10.1186/1471-2105-7-347 pmid:16842628 pmcid:PMC1539029 fatcat:tjj2jljkwbhw7mcl3ojbzeubmq

Database resources of the National Center for Biotechnology Information

E. W. Sayers, T. Barrett, D. A. Benson, E. Bolton, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, S. Federhen, M. Feolo, I. M. Fingerman (+31 others)
2011 Nucleic Acids Research  
PopSet and UniGene), proteins (Protein, the Conserved Domain Database (CDD), COBALT, Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB) and Protein Clusters) and  ...  This work is written by (a) US Government employee(s) and is in the public domain in the US.  ...  , protein and nucleotide sequences, chemicals (PDB heterogens), and conserved domains in the Conserved Domain Database (CDD) (41) .  ... 
doi:10.1093/nar/gkr1184 pmid:22140104 pmcid:PMC3245031 fatcat:zxmwupa435gfzcpusnv7oe3qnm

Database resources of the National Center for Biotechnology Information

D. L. Wheeler, T. Barrett, D. A. Benson, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, R. Edgar, S. Federhen, L. Y. Geer, Y. Kapustin (+18 others)
2007 Nucleic Acids Research  
In addition to maintaining the GenBank Õ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other  ...  biological data made available through the NCBI Web site.  ...  , protein domains from the Conserved Domain Database (CDD), and other gene-related resources.  ... 
doi:10.1093/nar/gkl1031 pmid:17170002 pmcid:PMC1781113 fatcat:pj7gnwwlpnbmza7c4ae7yatega

Database Resources of the National Center for Biotechnology Information

2016 Nucleic Acids Research  
In addition to maintaining the GenBank Õ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other  ...  biological data made available through the NCBI Web site.  ...  , protein domains from the Conserved Domain Database (CDD), and other gene-related resources.  ... 
doi:10.1093/nar/gkw1071 pmid:27899561 pmcid:PMC5210554 fatcat:itaqk5uwv5bv7gm7f55zunbcwq

Database resources of the National Center for Biotechnology Information

E. W. Sayers, T. Barrett, D. A. Benson, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, R. Edgar, S. Federhen, M. Feolo, L. Y. Geer (+21 others)
2009 Nucleic Acids Research  
Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases.  ...  RECENT DEVELOPMENTS Enhancements to PubMed searches Over the past year, NCBI has introduced several enhancements to the PubMed search interface and Abstract Plus views.  ...  from the Conserved Domain Database (CDD) and other gene-related resources.  ... 
doi:10.1093/nar/gkn741 pmid:18940862 pmcid:PMC2686545 fatcat:wbtxaka7ibbbdn7xj2ga7n46ge

Database resources of the National Center for Biotechnology Information

2012 Nucleic Acids Research  
In addition to maintaining the GenBank Õ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi. nlm.nih.gov) provides analysis and retrieval resources  ...  for the data in GenBank and other biological data made available through the NCBI web site.  ...  consortia; and internal curation efforts.  ... 
doi:10.1093/nar/gks1189 pmid:23193264 pmcid:PMC3531099 fatcat:hp2biq76anavbavtbbz4jcvwqm

The BioGRID Interaction Database: 2011 update

C. Stark, B.-J. Breitkreutz, A. Chatr-aryamontri, L. Boucher, R. Oughtred, M. S. Livstone, J. Nixon, K. Van Auken, X. Wang, X. Shi, T. Reguly, J. M. Rust (+3 others)
2010 Nucleic Acids Research  
BioGRID provides interaction data to several model organism databases, resources such as Entrez-Gene and other interaction meta-databases.  ...  Current curation drives are focused on particular areas of biology to enable insights into conserved networks and pathways that are relevant to human health.  ...  Judy Blake for support and helpful discussions.  ... 
doi:10.1093/nar/gkq1116 pmid:21071413 pmcid:PMC3013707 fatcat:5e7qa7hecfbnfj7o3dvxiw4yum

PaperBLAST: Text Mining Papers for Information about Homologs

Morgan N. Price, Adam P. Arkin, Morgan G. I. Langille
2017 mSystems  
Given a protein of interest, PaperBLAST quickly finds similar proteins that are discussed in the literature and presents snippets of text from relevant articles or from the curators.  ...  Then, given a protein of interest, it can quickly find similar proteins in its database by using standard software (BLAST), and it can show snippets of text from relevant papers.  ...  ACKNOWLEDGMENTS We thank Johanna McEntyre and Jee-Hyub Kim for advice on using EuropePMC. We thank Maximilian Haeussler for providing pubCrawl2. The  ... 
doi:10.1128/msystems.00039-17 pmid:28845458 pmcid:PMC5557654 fatcat:xpcwjz2qsnfarg5emlgnnwoyte
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