PubServer: literature searches by homology
PubServer, available at http://pubserver.burnham.org/, is a tool to automatically collect, filter and analyze publications associated with groups of homologous proteins. Protein entries in databases such as Entrez Protein database at NCBI contain information about publications associated with a give...
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| Format: | Online |
| Language: | English |
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Oxford University Press
2014
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086066/ |
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pubmed-40860662014-10-28 PubServer: literature searches by homology Jaroszewski, Lukasz Koska, Laszlo Sedova, Mayya Godzik, Adam Article PubServer, available at http://pubserver.burnham.org/, is a tool to automatically collect, filter and analyze publications associated with groups of homologous proteins. Protein entries in databases such as Entrez Protein database at NCBI contain information about publications associated with a given protein. The scope of these publications varies a lot: they include studies focused on biochemical functions of individual proteins, but also reports from genome sequencing projects that introduce tens of thousands of proteins. Collecting and analyzing publications related to sets of homologous proteins help in functional annotation of novel protein families and in improving annotations of well-studied protein families or individual genes. However, performing such collection and analysis manually is a tedious and time-consuming process. PubServer automatically collects identifiers of homologous proteins using PSI-Blast, retrieves literature references from corresponding database entries and filters out publications unlikely to contain useful information about individual proteins. It also prepares simple vocabulary statistics from titles, abstracts and MeSH terms to identify the most frequently occurring keywords, which may help to quickly identify common themes in these publications. The filtering criteria applied to collected publications are user-adjustable. The results of the server are presented as an interactive page that allows re-filtering and different presentations of the output. Oxford University Press 2014-07-01 2014-06-23 /pmc/articles/PMC4086066/ /pubmed/24957597 http://dx.doi.org/10.1093/nar/gku450 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Jaroszewski, Lukasz Koska, Laszlo Sedova, Mayya Godzik, Adam |
| spellingShingle |
Jaroszewski, Lukasz Koska, Laszlo Sedova, Mayya Godzik, Adam PubServer: literature searches by homology |
| author_facet |
Jaroszewski, Lukasz Koska, Laszlo Sedova, Mayya Godzik, Adam |
| author_sort |
Jaroszewski, Lukasz |
| title |
PubServer: literature searches by homology |
| title_short |
PubServer: literature searches by homology |
| title_full |
PubServer: literature searches by homology |
| title_fullStr |
PubServer: literature searches by homology |
| title_full_unstemmed |
PubServer: literature searches by homology |
| title_sort |
pubserver: literature searches by homology |
| description |
PubServer, available at http://pubserver.burnham.org/, is a tool to automatically
collect, filter and analyze publications associated with groups of homologous
proteins. Protein entries in databases such as Entrez Protein database at NCBI
contain information about publications associated with a given protein. The
scope of these publications varies a lot: they include studies focused on
biochemical functions of individual proteins, but also reports from genome
sequencing projects that introduce tens of thousands of proteins. Collecting and
analyzing publications related to sets of homologous proteins help in functional
annotation of novel protein families and in improving annotations of
well-studied protein families or individual genes. However, performing such
collection and analysis manually is a tedious and time-consuming process.
PubServer automatically collects identifiers of homologous proteins using
PSI-Blast, retrieves literature references from corresponding database entries
and filters out publications unlikely to contain useful information about
individual proteins. It also prepares simple vocabulary statistics from titles,
abstracts and MeSH terms to identify the most frequently occurring keywords,
which may help to quickly identify common themes in these publications. The
filtering criteria applied to collected publications are user-adjustable. The
results of the server are presented as an interactive page that allows
re-filtering and different presentations of the output. |
| publisher |
Oxford University Press |
| publishDate |
2014 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086066/ |
| _version_ |
1613109729554333696 |