The EXACT description of biomedical protocols

Motivation: Many published manuscripts contain experiment protocols which are poorly described or deficient in information. This means that the published results are very hard or impossible to repeat. This problem is being made worse by the increasing complexity of high-throughput/automated methods....

Full description

Saved in:
Bibliographic Details
Published in:Bioinformatics 2008-07, Vol.24 (13), p.i295-i303
Main Authors: Soldatova, Larisa N., Aubrey, Wayne, King, Ross D., Clare, Amanda
Format: Article
Language:English
Subjects:
Database Management Systems
Databases, Factual
Documentation - methods
Information Storage and Retrieval - methods
Internet
Research - classification
Research - standards
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
cited_by cdi_FETCH-LOGICAL-c612t-fbadd89a3e0eb2408317eb6f14295c3938dbeb89d93ca922bf5290f66d86b363
cites cdi_FETCH-LOGICAL-c612t-fbadd89a3e0eb2408317eb6f14295c3938dbeb89d93ca922bf5290f66d86b363
container_end_page i303
container_issue 13
container_start_page i295
container_title Bioinformatics
container_volume 24
creator Soldatova, Larisa N.
Aubrey, Wayne
King, Ross D.
Clare, Amanda
description Motivation: Many published manuscripts contain experiment protocols which are poorly described or deficient in information. This means that the published results are very hard or impossible to repeat. This problem is being made worse by the increasing complexity of high-throughput/automated methods. There is therefore a growing need to represent experiment protocols in an efficient and unambiguous way. Results: We have developed the Experiment ACTions (EXACT) ontology as the basis of a method of representing biological laboratory protocols. We provide example protocols that have been formalized using EXACT, and demonstrate the advantages and opportunities created by using this formalization. We argue that the use of EXACT will result in the publication of protocols with increased clarity and usefulness to the scientific community. Availability: The ontology, examples and code can be downloaded from http://www.aber.ac.uk/compsci/Research/bio/dss/EXACT/ Contact: Larisa Soldatova lss@aber.ac.uk
doi_str_mv 10.1093/bioinformatics/btn156
format article
fullrecord <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_2718634</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><oup_id>10.1093/bioinformatics/btn156</oup_id><sourcerecordid>69270968</sourcerecordid><originalsourceid>FETCH-LOGICAL-c612t-fbadd89a3e0eb2408317eb6f14295c3938dbeb89d93ca922bf5290f66d86b363</originalsourceid><addsrcrecordid>eNqNkUtP3DAUha2qqDzan1AUddFdGL8fm0owGqASEpuoGnVj2Y4Dppk42Akq_56gjKaFDax8JX_n3GMfAL4ieIKgIgsbYuiamDZmCC4v7NAhxj-AA0Q5LDFk6uM0Ey5KKiHZB4c530HIEKX0E9hHkkkusDgAZXXri9X6dFkVtc8uhX4IsStiU0wLNr4OzrRFn-IQXWzzZ7DXmDb7L9vzCFTnq2p5WV5dX_xcnl6VjiM8lI01dS2VIR56iymUBAlveYMoVswRRWRtvZWqVsQZhbFtGFaw4byW3BJOjsCP2bYf7ZTB-W5IptV9ChuTHnU0Qb-86cKtvokPGgskOaGTwfetQYr3o8-D3oTsfNuazscxa66wgIrLN0FCmGCIP0f69gq8i2Pqpk_QSEkhIMVogtgMuRRzTr7ZRUZQP7emX7am59Ym3fH_7_2n2tY0AXAG4ti_27OcJSEP_u9OZNIfzQURTF-uf2tEf1WC4DO9Jk-fNrj0</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>198770421</pqid></control><display><type>article</type><title>The EXACT description of biomedical protocols</title><source>Access via Oxford University Press (Open Access Collection)</source><source>PubMed Central</source><creator>Soldatova, Larisa N. ; Aubrey, Wayne ; King, Ross D. ; Clare, Amanda</creator><creatorcontrib>Soldatova, Larisa N. ; Aubrey, Wayne ; King, Ross D. ; Clare, Amanda</creatorcontrib><description>Motivation: Many published manuscripts contain experiment protocols which are poorly described or deficient in information. This means that the published results are very hard or impossible to repeat. This problem is being made worse by the increasing complexity of high-throughput/automated methods. There is therefore a growing need to represent experiment protocols in an efficient and unambiguous way. Results: We have developed the Experiment ACTions (EXACT) ontology as the basis of a method of representing biological laboratory protocols. We provide example protocols that have been formalized using EXACT, and demonstrate the advantages and opportunities created by using this formalization. We argue that the use of EXACT will result in the publication of protocols with increased clarity and usefulness to the scientific community. Availability: The ontology, examples and code can be downloaded from http://www.aber.ac.uk/compsci/Research/bio/dss/EXACT/ Contact: Larisa Soldatova lss@aber.ac.uk</description><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1460-2059</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btn156</identifier><identifier>PMID: 18586727</identifier><identifier>CODEN: BOINFP</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Database Management Systems ; Databases, Factual ; Documentation - methods ; Information Storage and Retrieval - methods ; Internet ; Research - classification ; Research - standards</subject><ispartof>Bioinformatics, 2008-07, Vol.24 (13), p.i295-i303</ispartof><rights>2008 The Author(s) 2008</rights><rights>2008 The Author(s)</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c612t-fbadd89a3e0eb2408317eb6f14295c3938dbeb89d93ca922bf5290f66d86b363</citedby><cites>FETCH-LOGICAL-c612t-fbadd89a3e0eb2408317eb6f14295c3938dbeb89d93ca922bf5290f66d86b363</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718634/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718634/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,1604,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18586727$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Soldatova, Larisa N.</creatorcontrib><creatorcontrib>Aubrey, Wayne</creatorcontrib><creatorcontrib>King, Ross D.</creatorcontrib><creatorcontrib>Clare, Amanda</creatorcontrib><title>The EXACT description of biomedical protocols</title><title>Bioinformatics</title><addtitle>Bioinformatics</addtitle><description>Motivation: Many published manuscripts contain experiment protocols which are poorly described or deficient in information. This means that the published results are very hard or impossible to repeat. This problem is being made worse by the increasing complexity of high-throughput/automated methods. There is therefore a growing need to represent experiment protocols in an efficient and unambiguous way. Results: We have developed the Experiment ACTions (EXACT) ontology as the basis of a method of representing biological laboratory protocols. We provide example protocols that have been formalized using EXACT, and demonstrate the advantages and opportunities created by using this formalization. We argue that the use of EXACT will result in the publication of protocols with increased clarity and usefulness to the scientific community. Availability: The ontology, examples and code can be downloaded from http://www.aber.ac.uk/compsci/Research/bio/dss/EXACT/ Contact: Larisa Soldatova lss@aber.ac.uk</description><subject>Database Management Systems</subject><subject>Databases, Factual</subject><subject>Documentation - methods</subject><subject>Information Storage and Retrieval - methods</subject><subject>Internet</subject><subject>Research - classification</subject><subject>Research - standards</subject><issn>1367-4803</issn><issn>1460-2059</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2008</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><recordid>eNqNkUtP3DAUha2qqDzan1AUddFdGL8fm0owGqASEpuoGnVj2Y4Dppk42Akq_56gjKaFDax8JX_n3GMfAL4ieIKgIgsbYuiamDZmCC4v7NAhxj-AA0Q5LDFk6uM0Ey5KKiHZB4c530HIEKX0E9hHkkkusDgAZXXri9X6dFkVtc8uhX4IsStiU0wLNr4OzrRFn-IQXWzzZ7DXmDb7L9vzCFTnq2p5WV5dX_xcnl6VjiM8lI01dS2VIR56iymUBAlveYMoVswRRWRtvZWqVsQZhbFtGFaw4byW3BJOjsCP2bYf7ZTB-W5IptV9ChuTHnU0Qb-86cKtvokPGgskOaGTwfetQYr3o8-D3oTsfNuazscxa66wgIrLN0FCmGCIP0f69gq8i2Pqpk_QSEkhIMVogtgMuRRzTr7ZRUZQP7emX7am59Ym3fH_7_2n2tY0AXAG4ti_27OcJSEP_u9OZNIfzQURTF-uf2tEf1WC4DO9Jk-fNrj0</recordid><startdate>20080701</startdate><enddate>20080701</enddate><creator>Soldatova, Larisa N.</creator><creator>Aubrey, Wayne</creator><creator>King, Ross D.</creator><creator>Clare, Amanda</creator><general>Oxford University Press</general><general>Oxford Publishing Limited (England)</general><scope>BSCLL</scope><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QF</scope><scope>7QO</scope><scope>7QQ</scope><scope>7SC</scope><scope>7SE</scope><scope>7SP</scope><scope>7SR</scope><scope>7TA</scope><scope>7TB</scope><scope>7TM</scope><scope>7TO</scope><scope>7U5</scope><scope>8BQ</scope><scope>8FD</scope><scope>F28</scope><scope>FR3</scope><scope>H8D</scope><scope>H8G</scope><scope>H94</scope><scope>JG9</scope><scope>JQ2</scope><scope>K9.</scope><scope>KR7</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>P64</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20080701</creationdate><title>The EXACT description of biomedical protocols</title><author>Soldatova, Larisa N. ; Aubrey, Wayne ; King, Ross D. ; Clare, Amanda</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c612t-fbadd89a3e0eb2408317eb6f14295c3938dbeb89d93ca922bf5290f66d86b363</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2008</creationdate><topic>Database Management Systems</topic><topic>Databases, Factual</topic><topic>Documentation - methods</topic><topic>Information Storage and Retrieval - methods</topic><topic>Internet</topic><topic>Research - classification</topic><topic>Research - standards</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Soldatova, Larisa N.</creatorcontrib><creatorcontrib>Aubrey, Wayne</creatorcontrib><creatorcontrib>King, Ross D.</creatorcontrib><creatorcontrib>Clare, Amanda</creatorcontrib><collection>Istex</collection><collection>Access via Oxford University Press (Open Access Collection)</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Aluminium Industry Abstracts</collection><collection>Biotechnology Research Abstracts</collection><collection>Ceramic Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>Corrosion Abstracts</collection><collection>Electronics &amp; Communications Abstracts</collection><collection>Engineered Materials Abstracts</collection><collection>Materials Business File</collection><collection>Mechanical &amp; Transportation Engineering Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>ANTE: Abstracts in New Technology &amp; Engineering</collection><collection>Engineering Research Database</collection><collection>Aerospace Database</collection><collection>Copper Technical Reference Library</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Materials Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>ProQuest Health &amp; Medical Complete (Alumni)</collection><collection>Civil Engineering Abstracts</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts – Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Soldatova, Larisa N.</au><au>Aubrey, Wayne</au><au>King, Ross D.</au><au>Clare, Amanda</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The EXACT description of biomedical protocols</atitle><jtitle>Bioinformatics</jtitle><addtitle>Bioinformatics</addtitle><date>2008-07-01</date><risdate>2008</risdate><volume>24</volume><issue>13</issue><spage>i295</spage><epage>i303</epage><pages>i295-i303</pages><issn>1367-4803</issn><eissn>1460-2059</eissn><eissn>1367-4811</eissn><coden>BOINFP</coden><abstract>Motivation: Many published manuscripts contain experiment protocols which are poorly described or deficient in information. This means that the published results are very hard or impossible to repeat. This problem is being made worse by the increasing complexity of high-throughput/automated methods. There is therefore a growing need to represent experiment protocols in an efficient and unambiguous way. Results: We have developed the Experiment ACTions (EXACT) ontology as the basis of a method of representing biological laboratory protocols. We provide example protocols that have been formalized using EXACT, and demonstrate the advantages and opportunities created by using this formalization. We argue that the use of EXACT will result in the publication of protocols with increased clarity and usefulness to the scientific community. Availability: The ontology, examples and code can be downloaded from http://www.aber.ac.uk/compsci/Research/bio/dss/EXACT/ Contact: Larisa Soldatova lss@aber.ac.uk</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>18586727</pmid><doi>10.1093/bioinformatics/btn156</doi><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 1367-4803
ispartof Bioinformatics, 2008-07, Vol.24 (13), p.i295-i303
issn 1367-4803
1460-2059
1367-4811
language eng
recordid cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_2718634
source Access via Oxford University Press (Open Access Collection); PubMed Central
subjects Database Management Systems
Databases, Factual
Documentation - methods
Information Storage and Retrieval - methods
Internet
Research - classification
Research - standards
title The EXACT description of biomedical protocols
url http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-03T19%3A15%3A40IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=The%20EXACT%20description%20of%20biomedical%20protocols&rft.jtitle=Bioinformatics&rft.au=Soldatova,%20Larisa%20N.&rft.date=2008-07-01&rft.volume=24&rft.issue=13&rft.spage=i295&rft.epage=i303&rft.pages=i295-i303&rft.issn=1367-4803&rft.eissn=1460-2059&rft.coden=BOINFP&rft_id=info:doi/10.1093/bioinformatics/btn156&rft_dat=%3Cproquest_pubme%3E69270968%3C/proquest_pubme%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c612t-fbadd89a3e0eb2408317eb6f14295c3938dbeb89d93ca922bf5290f66d86b363%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=198770421&rft_id=info:pmid/18586727&rft_oup_id=10.1093/bioinformatics/btn156&rfr_iscdi=true