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Concept-based annotation of enzyme classes

O. Hofmann, D. Schomburg
<span title="2005-01-20">2005</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Assignments between enzyme classes and diseases were created based on their co-occurrence within a single sentence.  ...  We describe a method to automatically annotate enzyme classes with disease-related information extracted from the biomedical literature for inclusion in such a database.  ...  We are particularly thankful to the curators of the BRENDA database for their assistance during the implementation and evaluation of this system.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bti284">doi:10.1093/bioinformatics/bti284</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15661799">pmid:15661799</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zx5bunzib5d2nnjdoselc7poce">fatcat:zx5bunzib5d2nnjdoselc7poce</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180728164150/https://watermark.silverchair.com/bti284.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAb4wggG6BgkqhkiG9w0BBwagggGrMIIBpwIBADCCAaAGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMZX6KIHj3FjwR7tDKAgEQgIIBcQ6fclNhp7hCLjJqm3qzZurouLAJgfMBUxyC6GaUYUfvS3FRi8RjfGgvrGkVCrB2HrxzEH_pwHI1j6Qg9xIcrFr_GlXBOTQ-VzeQlVgAvMUoCzN2o4_bh_mBPmOfwyOUilUulVuhrDa5QKAcvud1s-reib_eqkDgsvXwccs7fe8enbeUb1J1D0iItEc8FWAIA2r3QSXTTHdFC8dt9fjDDtalt_RNdoZijlyrZxMWm3raS4AugXC65NZm-LT9NQMMbHehClnAgBFXgO7w2q89Pfrv_6_lRO1NGQ02kylTvqMXQnf9mCpw0DRtT9Lm4C5oXqE6Ftk4fibrjag0d68HmF87DiaYo63JqMiW-zI4baOPsBSUJheifAn3ClQS54E62ooIM0qFSj45gibC-IqQZLzIK4rNJoTVjjC5s-T9QOIKll-DQrbiRaC5CiW0jC6yawG3YEPtSLAKnqu3ycHh6JcqHoWDZaprayZMHPTakNgYQA" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/64/b6/64b65eae51a02ac5319c8362038f2e1706d79f0a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bti284"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Gene Ontology-Based Annotation Analysis and Categorization of Metabolic Pathways

Ali Cakmak, Mustafa Kirac, Marc R. Reynolds, Zehra M. Ozsoyoglu, Gultekin Ozsoyoglu
<span title="">2007</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hrd3w4j23bhqjk57onfefnx7me" style="color: black;">International Conference on Scientific and Statistical Database Management</a> </i> &nbsp;
In this paper, we present and evaluate computational techniques for categorizing pathways, based upon the Gene Ontology (GO) annotations of enzymes within metabolic pathways.  ...  Our approach is to use the notion of functionality templates, GO-functional graphs of pathways.  ...  Usually, each enzyme is annotated with a set of concepts from GO.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/ssdbm.2007.35">doi:10.1109/ssdbm.2007.35</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/ssdbm/CakmakKROO07.html">dblp:conf/ssdbm/CakmakKROO07</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cq75nxxnv5gkhknp3zuyb3n4oy">fatcat:cq75nxxnv5gkhknp3zuyb3n4oy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170705085242/http://sehir.edu.tr/alicakmak/Pages/pubs/Annotation%20Analysis%20and%20Categorization%20of%20Pathways.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/29/ef/29efb5528f1fbeaa931ad7805e10640b98157318.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/ssdbm.2007.35"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

A METHODOLOGY TO MIGRATE THE GENE ONTOLOGY TO A DESCRIPTION LOGIC ENVIRONMENT USING DAML+OIL

C. J. WROE, R. STEVENS, C. A. GOBLE, M. ASHBURNER
<span title="">2002</span> <i title="WORLD SCIENTIFIC"> Biocomputing 2003 </i> &nbsp;
The Gene Ontology Next Generation Project (GONG) is developing a staged methodology to evolve the current representation of the Gene Ontology into DAML+OIL in order to take advantage of the richer formal  ...  expressiveness and the reasoning capabilities of the underlying description logic.  ...  We would like to thank Midori Harris and Jane Lomax of the GO Consortium Editorial Team for their advice and guidance.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/9789812776303_0058">doi:10.1142/9789812776303_0058</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gjsw2sveebaebbt3fabwy7kz44">fatcat:gjsw2sveebaebbt3fabwy7kz44</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20070626220919/http://psb.stanford.edu/psb-online/proceedings/psb03/wroe.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/97/95/9795cf5de5463b632093be9c440f1e9a79237504.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/9789812776303_0058"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> worldscientific.com </button> </a>

The FungalWeb Ontology: Semantic Web Challenges in Bioinformatics and Genomics [chapter]

Arash Shaban-Nejad, Christopher J. O. Baker, Volker Haarslev, Greg Butler
<span title="">2005</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
The classification of fungi presented in the ontology is based on phylum, class, order, family, genus and species. Species are considered as the fungi instances.  ...  Enzymes are classified based on catalyzed reactions recommended by the International Union of Biochemistry and Molecular Biology (IUBMB). Enzyme names are defined as the enzyme instances.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/11574620_78">doi:10.1007/11574620_78</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gu6bzj6u6zhmhfivwynyoulv5m">fatcat:gu6bzj6u6zhmhfivwynyoulv5m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180725041451/https://link.springer.com/content/pdf/10.1007%2F11574620_78.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f8/5b/f85bba2ba6536e68f8ffd8ef69707aebbc3ea12d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/11574620_78"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Evaluation of high-throughput functional categorization of human disease genes

James L Chen, Yang Liu, Lee T Sam, Jianrong Li, Yves A Lussier
<span title="">2007</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
The second method was based on the similarity of human disease genes clustered according to the information-theoretic distance of their Gene Ontology annotations.  ...  and particularly in the utilization of these annotations.  ...  The full contents of the supplement are available online at http://www.biomedcentral.com/ 1471-2105/8?issue=S3.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-8-s3-s7">doi:10.1186/1471-2105-8-s3-s7</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17493290">pmid:17493290</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1892104/">pmcid:PMC1892104</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fnx5dv6im5atvjwxth5u6hsaku">fatcat:fnx5dv6im5atvjwxth5u6hsaku</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170913190304/https://link.springer.com/content/pdf/10.1186%2F1471-2105-8-S3-S7.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a4/61/a461a03e623a23bb8f538194cf53566e152066c0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-8-s3-s7"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1892104" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Semantic annotation of biological concepts interplaying microbial cellular responses

Rafael Carreira, Sónia Carneiro, Rui Pereira, Miguel Rocha, Isabel Rocha, Eugénio C Ferreira, Anália Lourenço
<span title="">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
The corpus consists of 130 full-text papers with a total of 59043 annotations for 3649 different biomedical concepts; the two dominant classes are genes (highest number of unique concepts) and compounds  ...  (most frequently annotated concepts), whereas other important cellular concepts such as proteins account for no more than 10% of the annotated concepts.  ...  "luciferin" which is a class of small-molecules that are oxidized in the presence of the enzyme luciferase to produce oxyluciferin and energy in the form of light).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-12-460">doi:10.1186/1471-2105-12-460</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22122862">pmid:22122862</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3259143/">pmcid:PMC3259143</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mj6to5arrfav5mkn6fddhy7lgy">fatcat:mj6to5arrfav5mkn6fddhy7lgy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170815005422/http://repositorium.sdum.uminho.pt/bitstream/1822/16826/1/1471-2105-12-460.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/df/b1/dfb1dd419135a9d3dbc6275dec01da0de16e2d2e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-12-460"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3259143" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Stringent response of Escherichia coli: revisiting the bibliome using literature mining

Sónia Carneiro, Anália Lourenço, Eugénio C Ferreira, Isabel Rocha
<span title="">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hmb3j5fj5rgnzgpqjnnt2msoyu" style="color: black;">Microbial Informatics and Experimentation</a> </i> &nbsp;
In addition, the identification of less annotated concepts revealed that some (p) ppGpp-induced functional activities are still overlooked in most reviews.  ...  Such accumulation is known to be controlled by the activity of two enzymes, the ribosome-bound RelA enzyme (ppGpp synthetase I) that synthesises (p)ppGpp nucleotides  ...  SC performed the annotations of biological concepts in the full-text documents. AL performed the corpus analysis and ECF supervised most of the statistical analysis.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2042-5783-1-14">doi:10.1186/2042-5783-1-14</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22587779">pmid:22587779</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3372295/">pmcid:PMC3372295</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/45nynfublvdhrk44etzvd6muyy">fatcat:45nynfublvdhrk44etzvd6muyy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170922011802/https://microbialinformaticsj.biomedcentral.com/track/pdf/10.1186/2042-5783-1-14?site=microbialinformaticsj.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/62/5d/625da4434edf140085f4c5a735d9a9e210959577.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2042-5783-1-14"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372295" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Semantic reclassification of the UMLS concepts

J.-W. Fan, C. Friedman
<span title="2008-07-13">2008</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
To benefit applications using the semantic classification of the Unified Medical Language System (UMLS) concepts, we automatically reclassified the concepts based on their lexical and contextual features  ...  Accurate semantic classification is valuable for text mining and knowledge-based tasks that perform inference based on semantic classes.  ...  Funding: This work was supported by Grants R01 LM7659 and R01 LM8635 from the National Library of Medicine of USA. Conflict of Interest: none declared.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btn343">doi:10.1093/bioinformatics/btn343</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18625612">pmid:18625612</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2519163/">pmcid:PMC2519163</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xw3io2ay7fdmtetfflb2k3zvxm">fatcat:xw3io2ay7fdmtetfflb2k3zvxm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200511062621/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC2519163&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/52/37/52378c0b5a78543b28137b9f4cfa04518f00cabd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btn343"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2519163" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology

Goksel Misirli, Anil Wipat, Joseph Mullen, Katherine James, Matthew Pocock, Wendy Smith, Nick Allenby, Jennifer S. Hallinan
<span title="2013-06-01">2013</span> <i title="Walter de Gruyter GmbH"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fvl4m6o2tre4pcvl4ljymxu4ly" style="color: black;">Journal of Integrative Bioinformatics</a> </i> &nbsp;
SummaryBacillOndex is an extension of the Ondex data integration system, providing a semantically annotated, integrated knowledge base for the model Gram-positive bacterium Bacillus subtilis.  ...  We describe the process of creating a BacillOndex instance, and describe the use of the system for the analysis of single nucleotide polymorphisms in B. subtilis Marburg.  ...  protein complex concepts representing gene products and their aggregates; • COG class, COG class category, KEGG orthologs enzyme (KOEN), KEGG orthologs gene (KOGE) and KEGG orthologs protein (KOPR) concepts  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1515/jib-2013-224">doi:10.1515/jib-2013-224</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rjgfosb52zddxeg3uhxtmvwhty">fatcat:rjgfosb52zddxeg3uhxtmvwhty</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201201232527/https://www.degruyter.com/downloadpdf/journals/jib/10/2/article-p103.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d7/82/d782fe5616759f3d222c642741e3fa03404ccf54.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1515/jib-2013-224"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> degruyter.com </button> </a>

BacillOndex: an integrated data resource for systems and synthetic biology

Goksel Misirli, Anil Wipat, Joseph Mullen, Katherine James, Matthew Pocock, Wendy Smith, Nick Allenby, Jennifer S Hallinan
<span title="2013-04-10">2013</span> <i title="Walter de Gruyter GmbH"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fvl4m6o2tre4pcvl4ljymxu4ly" style="color: black;">Journal of Integrative Bioinformatics</a> </i> &nbsp;
BacillOndex is an extension of the Ondex data integration system, providing a semantically annotated, integrated knowledge base for the model Gram-positive bacterium Bacillus subtilis.  ...  We describe the process of creating a BacillOndex instance, and describe the use of the system for the analysis of single nucleotide polymorphisms in B. subtilis Marburg.  ...  protein complex concepts representing gene products and their aggregates; • COG class, COG class category, KEGG orthologs enzyme (KOEN), KEGG orthologs gene (KOGE) and KEGG orthologs protein (KOPR) concepts  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2390/biecoll-jib-2013-224">doi:10.2390/biecoll-jib-2013-224</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23571273">pmid:23571273</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fzb2gjmccbfj3jccbr33jxuuyy">fatcat:fzb2gjmccbfj3jccbr33jxuuyy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200226090948/https://www.degruyter.com/downloadpdf/j/jib.2013.10.issue-2/biecoll-jib-2013-224/biecoll-jib-2013-224.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2390/biecoll-jib-2013-224"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Metabolic Pathway Assignment of Plant Genes based on Phylogenetic Profiling–A Feasibility Study

Sandra Weißenborn, Dirk Walther
<span title="2017-10-27">2017</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/bbmitkj3efgeppizzjrx6w5emu" style="color: black;">Frontiers in Plant Science</a> </i> &nbsp;
We determined phylogenetic profiles for 40,960 metabolic pathway enzyme genes with assigned EC numbers from 24 plant species based on sequence and pathway annotation data from KEGG and Ensembl Plants.  ...  database and established gene families based on pairwise sequence identities and annotation information.  ...  ACKNOWLEDGMENTS We wish to acknowledge the helpful comments provided by Celine Vens, Dragi Kovev, and Saso Dzeroski on the use of the CLUS software and the interpretation its results.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fpls.2017.01831">doi:10.3389/fpls.2017.01831</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29163570">pmid:29163570</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5664361/">pmcid:PMC5664361</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gwdw3f5oejetjiseq7ts3sdxj4">fatcat:gwdw3f5oejetjiseq7ts3sdxj4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190303064633/http://pdfs.semanticscholar.org/b119/c093b53077ff589c6c61d1a951b048cc638d.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b1/19/b119c093b53077ff589c6c61d1a951b048cc638d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fpls.2017.01831"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5664361" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Association algorithm to mine the rules that govern enzyme definition and to classify protein sequences

Shih-Hau Chiu, Chien-Chi Chen, Gwo-Fang Yuan, Thy-Hou Lin
<span title="2006-06-15">2006</span> <i title="Springer (Biomed Central Ltd.)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
These were otherwise poorly annotated using their functional descriptions. The feasibility of using the method presented here to classify enzyme classes based on the enzyme domain rules is evident.  ...  The fungus training dataset which lacks an enzyme class description was also used to evaluate the fungus candidate rules. A total of 88 out of 5085 test entries were matched with the fungus rule set.  ...  This work is financially supported by the grant from the Ministry of Economic Affairs (Project No. 93-EC-17-A-17-R7-0563) to Food Industry Research and Development Institute.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-7-304">doi:10.1186/1471-2105-7-304</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16776838">pmid:16776838</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1552092/">pmcid:PMC1552092</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2v2tloebafgnzcdbksvuzk7enq">fatcat:2v2tloebafgnzcdbksvuzk7enq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200210172500/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC1552092&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/95/fb/95fb36281e57b8d2e8e7cba8976d821ccd7cd8d2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-7-304"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1552092" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations

Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf
<span title="2018-06-27">2018</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
We propose the Onto2Vec method, an approach to learn feature vectors for biological entities based on their annotations to biomedical ontologies.  ...  Our method can be applied to a wide range of bioinformatics research problems such as similarity-based prediction of interactions between proteins, classification of interaction types using supervised  ...  ontology concepts that e 1 is annotated with, S 2 is the set of concepts that e 2 is annotated with, and sim(c 1 , c 2 ) is the similarity value between concept c 1 and concept c 2 , which could have  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bty259">doi:10.1093/bioinformatics/bty259</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29949999">pmid:29949999</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6022543/">pmcid:PMC6022543</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nmb7uxfcgzhpvix3ccczi3hlge">fatcat:nmb7uxfcgzhpvix3ccczi3hlge</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180424204000/http://repository.kaust.edu.sa/kaust/bitstream/10754/627122/1/1802.00864v1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/82/23/82234623b1ff2047ee166bd457c06c5c82642ae2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bty259"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022543" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

DrugProt corpus chemicals and drugs annotation guidelines [CHEMDNER - Biocreative IV]

Obdulia Rabal, Martin Krallinger
<span title="2021-06-15">2021</span> <i title="Zenodo"> Zenodo </i> &nbsp;
Introduction The annotation guidelines have been refined after iterative cycles of annotations of sample documents.  ...  Annotation guidelines (and data selection criteria) used for the annotations of chemical entities of the CHEMDNER, ChemProt and DrugProt corpora.  ...  with Enzymes Mentions of CEM that are part of mentions of enzymes should be tagged. i.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.4957519">doi:10.5281/zenodo.4957519</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3ltiuyqkpfgpxewwqtn4rhfdku">fatcat:3ltiuyqkpfgpxewwqtn4rhfdku</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210623051916/https://zenodo.org/record/4957519/files/CEM_guidelines.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/cb/c7/cbc7c26a03dcbc12b4b19942d7ca0f6540a6df57.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.4957519"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> zenodo.org </button> </a>

Metabolic Network Analysis: Implication And Application

Syed Rahman, Pardha Jonnalagadda, Jyothi Padiadpu, Kai Hartmann, Rainer Schrader, Dietmar Schomburg
<span title="">2005</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
We introduce a new concept of "load points" for identifying and empirically ranking the important points (metabolites/enzymes) in the network.  ...  Identifying such enzymes is the key to network-based potential drug targeting [3] .  ...  We introduce a new concept of "load points" for identifying and empirically ranking the important points (metabolites/enzymes) in the network.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-6-s3-s12">doi:10.1186/1471-2105-6-s3-s12</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/62v7rmrl2bhlvjflqnl2zlq5be">fatcat:62v7rmrl2bhlvjflqnl2zlq5be</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720003009/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-6-S3-S12" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c2/80/c280d58baf70fc2e1cabfe90ffa73827d22ac81c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-6-s3-s12"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>
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