http://precedings.nature.com/tags/literature%20mining Recently posted documents tagged with 'literature mining' Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://dx.doi.org/10.1038/npre.2009.3491.1 PubMed articles are annotated using the Medical Subject Headings (MeSH) to increase search efficiency. However, MeSH contains limited information on many biomedical domains (e.g., vaccine). Biomedical ontologies may be used to improve PubMed searching capability. This study demonstrates that Vaccine Ontology (VO) can be used to significantly improve PubMed searching efficacy in the vaccine domain. The recall and precision of the ontology-based literature mining approach are analyzed and discussed. http://dx.doi.org/10.1038/npre.2009.3491.1 Tue, 28 Jul 2009 14:32:42 UTC Improvement of PubMed Literature Searching using Biomedical Ontology doi:10.1038/npre.2009.3491.1 2009-07-28 Zuoshuang Xiang Nature Precedings 2009-07-28T14:32:42Z Poster Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3134.1 The concept of community annotation is a growing discipline for achieving participation of the research community in depositing up‐to‐date knowledge in biological databases.The Solanaceae Genomics Network (SGN) is a clade‐oriented database (COD) focusing on plants of the nightshade family, including tomato, potato, pepper, eggplant, and tobacco, and is one of the bioinformatics nodes of the international tomato genome sequencing project. One of our major efforts is linking Solanaceae phenotype information with the underlying genes, and subsequently the genome. As part of this goal, SGN has introduced a database for locus names and descriptors, and a database for phenotypes of natural and induced variation. These two databases have web interfaces that allow cross references, associations with tomato gene models, and in‐house curated information of sequences, literature, ontologies, gene networks, and the Solanaceae biochemical pathways database (SolCyc). All of our curator tools are open for online community annotation, through specially assigned “submitter” accounts. Currently the community database consists of 5,548 phenotyped accessions, and 5,739 curated loci, out of which more than 300 loci where contributed or annotated by 66 active submitters, creating a database that is truly community driven.This framework is easily adaptable for other projects working on other taxa (for example see http://chlamybase.org), greatly expanding the application of this user‐friendly online annotation system. Community participation is fostered by an active outreach program that includes contacting potential submitters via emails, at meetings and conferences, and by promoting featured user submitted annotations on the SGN homepage. The source code and database schema for all SGN functionalities are freely available. Please contact SGN at sgn‐feedback[at]sgn.cornell.edu for more information. http://dx.doi.org/10.1038/npre.2009.3134.1 Wed, 22 Apr 2009 21:15:52 UTC The SOL Genomics Network Model: Making Community Annotation Work doi:10.1038/npre.2009.3134.1 2009-04-22 Naama Menda Nature Precedings 2009-04-22T21:15:52Z Poster Bioinformatics Plant Biology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3127.1 WormBase is the major public online database resource for the Caenorhabditis research community. The database was developed primarily for the nematode C. elegans but expanded to host genomes and biological data from other closely related nematode species including C. briggsae, C. remanei, C. brenneri, C. japonica and Pristionchus pacificus. WormBase has developed tools to mine the data held within the database and compare the hosted species. Over the years we have developed a variety of curation pipelines which often begin in a “first-pass” literature curation step. This involves a brief overview of the literature before directing it to specialised data curators who extract all relevant information. Curators focus on particular data types or experimental techniques such as gene structure changes (see the Sequence curation poster), variations, phenotypes or RNAi and their expertise in these fields make curation efficient. WormBase works with many other groups and consortiums to validate, process and integrate both large and small scale data resources. WormBase also provides data that will be of interest to the wider biomedical and bioinformatics communities allowing researchers to utilise the information and techniques offered by nematodes to study wider aspects including medicine and disease. http://dx.doi.org/10.1038/npre.2009.3127.1 Wed, 22 Apr 2009 15:12:30 UTC WormBase – Nematode Biology and Genomes doi:10.1038/npre.2009.3127.1 2009-04-22 Paul Davis Nature Precedings 2009-04-22T15:12:30Z Poster Genetics & Genomics Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/2101/version/2 With increasing number of bio-literature search engines, scientists and health professionals either make a subjective choice of tool(s) or face a challenge of analyzing multiple features of a plethora of bibliographic software. There is an urgent need for a thorough comparative analysis of the available literature scanning tools, from the user’s perspective. We report results of the first time semi-quantitative comparison of 21 search programs, which can search published (partial or full text) documents in life science areas. The observations can assist life science researchers and medical professionals to make an informed selection among the programs, depending on their search objectives. Some of the important findings are: 1. Most of the hits obtained from Scopus, ReleMed, EBImed, CiteXplore, and HighWire Press were usually relevant (i.e., these tools showed a better precision than other tools). 2. But a very high number of relevant citations were retrieved by HighWire Press, Google Scholar, CiteXplore and Pubmed Central (they had better recall). 3. HWP and CiteXplore seemed to have a good balance of precision and recall efficiencies. 4. PubMed Central, PubMed and Scopus provided the most useful query systems. 5. GoPubMed, BioAsk, EBIMed, ClusterMed could be more useful among the tools that can automatically process the retrieved citations for further scanning of bio-entities such as proteins, diseases, tissues, molecular interactions etc). The authors suggest the use of PubMed, Scopus, Google Scholar and HighWire Press – for better coverage, and GoPubMed – to view the hits categorized based on the MeSH and gene ontology terms. http://precedings.nature.com/documents/2101/version/2 Thu, 24 Jul 2008 15:38:26 UTC How do you choose your literature search tool(s)? hdl:10101/npre.2008.2101.2 2008-07-24 Kshitish K. Acharya Nature Precedings 2008-07-24T15:38:26Z Manuscript Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/2101/version/1 With increasing number of bibliographic software, scientists and health professionals either make a subjective choice of tool(s) that could suit their needs or face a challenge of analyzing multiple features of a plethora of search programs. There is an urgent need for a thorough comparative analysis of the available bio-literature scanning tools, from the user’s perspective. We report results of the first time semi-quantitative comparison of 21 programs, which can search published (partial or full text) documents in life science areas. The observations can assist life science researchers and medical professionals to make an informed selection among the programs, depending on their search objectives. Some of the important findings are: 1. Most of the hits obtained from Scopus, ReleMed, EBImed, CiteXplore, and HighWire Press were usually relevant (i.e. these tools show a better precision than other tools). 2. But a very high number of relevant citations were retrieved by HighWire Press, Google Scholar, CiteXplore and Pubmed Central (they had better recall). 3. HWP and CiteXplore seemed to have a good balance of precision and recall efficiencies. 4. PubMed Central, PubMed and Scopus provided the most useful query systems. 5. GoPubMed, BioAsk, EBIMed, ClusterMed could be more useful among the tools that can automatically process the retrieved citations for further scanning of bio-entities such as proteins, diseases, tissues, molecular interactions, etc. The authors suggest the use of PubMed, Scopus, Google Scholar and HighWire Press – for better coverage, and GoPubMed – to view the hits categorized based on the MeSH and gene ontology terms. The article is relavant to all life science subjects. http://precedings.nature.com/documents/2101/version/1 Tue, 22 Jul 2008 10:50:58 UTC A comparative analysis of 21 literature search engines hdl:10101/npre.2008.2101.1 2008-07-22 Kshitish K. Acharya Nature Precedings 2008-07-22T10:50:58Z Manuscript Bioinformatics http://creativecommons.org/licenses/by/3.0/