Difference between revisions of "Related Publications"

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==2013==
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* Cooper and Walls et al (2013). '''[http://pcp.oxfordjournals.org/content/54/2/e1.full The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses]'''. Plant and Cell Physiology 54: e1–e1
  
 +
==2012==
 +
* Lens et al. 2012. '''An extension of the Plant Ontology project supporting wood anatomy and development research.''' [http://bio.kuleuven.be/sys/iawa/IAWA%20J%20pdf%27s/33.no1-4.2012/IAWA%20J%2033%20%282%29%20113-117.pdf IAWA Journal] 33: 113–117.
  
 +
* Walls et al (2012). '''A plant disease extension of the Infectious Disease Ontology.''' In ''[http://ceur-ws.org/Vol-897/ Proceedings 3rd International Conference on Biomedical Ontology]'', Medical University of Graz, Graz, Austria.
 +
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* Arnaud, et al (2012). '''Towards a Reference Plant Trait Ontology for Modeling Knowledge of Plant Traits and Phenotypes'''. Proceedings of the International Conference on Knowledge Engineering and Ontology Development. Barcelona, Spain, pp 220–225
 +
 +
* Walls et al (2012). '''Ontologies as integrative tools for plant science.''' [http://www.amjbot.org/content/99/8/1263 American Journal of Botany] 99: 1263 –1275 (special invited paper).
  
 
==2008==
 
==2008==
 +
*Ilic et al, 2008. '''Plant Structure Ontology (PSO) - A morphological and anatomical ontology of flowering plants.''' In ''Anatomy Ontologies for Bioinformatics'', Springer, p 27-42. [http://www.springer.com/computer/computational+biology+and+bioinformatics/book/978-1-84628-884-5 Book]
  
 +
*Avraham et al, 2008.'''The Plant Ontology Database: a community resource for plant structure and development stages controlled vocabulary and annotations.''' [http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D449 Abstract] [http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D449 Full Text]]<br />[http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D449 Nucleic Acid Research], 36(Database issue):D449-D454
  
 
==2007==
 
==2007==
 
*The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration”, Nature Biotechnology,25 (11), November 2007, 1251 -1255. [[http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf Smith et al, 2007]]
 
*The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration”, Nature Biotechnology,25 (11), November 2007, 1251 -1255. [[http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf Smith et al, 2007]]
  
−
 
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*Ilic et al, 2007.'''The Plant Structure Ontology, a unified vocabulary of anatomy and morphology of a flowering plant.''' [[http://www.plantphysiol.org/cgi/content/abstract/143/2/587 Abstract]] [[http://www.plantphysiol.org/cgi/content/full/143/2/587 Full Text]]<br />[http://www.plantphysiol.org/ Plant Physiology], 2007, 143: 587-599 <br />
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*Plant Structure Ontology (PSO) - A morphological and anatomical ontology of flowering plants. In ''Anatomy Ontologies for Bioinformatics'', Springer, 2008, p 27-42. [[http://www.springer.com/computer/computational+biology+and+bioinformatics/book/978-1-84628-884-5 Book]]<br />
 
−
 
 
−
*The Plant Ontology Database: a community resource for plant structure and development stages controlled vocabulary and annotations. [[http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D449 Abstract]] [[http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D449 Full Text]]<br />[http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D449 Nucleic Acid Research], 2008, 36(Database issue):D449-D454<br />
 
−
 
 
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*The Plant Structure Ontology, a unified vocabulary of anatomy and morphology of a flowering plant. [[http://www.plantphysiol.org/cgi/content/abstract/143/2/587 Abstract]] [[http://www.plantphysiol.org/cgi/content/full/143/2/587 Full Text]]<br />[http://www.plantphysiol.org/ Plant Physiology], 2007, 143: 587-599 <br />
 
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*Whole-plant growth stage ontology for angiosperms and its application in plant biology. [[http://www.plantphysiol.org/cgi/content/abstract/142/2/414 Abstract]] [[http://www.plantphysiol.org/cgi/content/full/142/2/414 Full Text]]<br />[http://www.plantphysiol.org/ Plant Physiology], 2006, 142: 414-428
 
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*Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages. [[http://www.hindawi.com/GetArticle.aspx?doi=10.1002/cfg.496&e=CTA Abstract]] [[http://www.hindawi.com/GetPDF.aspx?doi=10.1002/cfg.496 Full Text]]<br />[http://www3.interscience.wiley.com/cgi-bin/jhome/77002016 Comparative and Functional Genomics], 2005, Volume 6(7-8), 388 - 397
 
−
 
 
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*The Gene Ontology (GO) database and informatics resource. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14681407 Abstract]] [[http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D258 Full Text]] <br />[http://nar.oupjournals.org/ Nucleic Acids Research], 2004, Vol 32: D258-D261.
 
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*Bio-ontologies-fast and furious. [[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v22/n6/full/nbt0604-773.html Full Text]] <br />[http://www.nature.com/nbt/ Nature Biotechnology], 2004, Vol 22(6): 773-774.
 
  
 
==2006==
 
==2006==
Line 29: Line 26:
 
*Ontologies for data and knowledge sharing in biology: plant ROS signaling as a case study. [[http://www3.interscience.wiley.com/cgi-bin/abstract/112279243/ABSTRACT?CRETRY=1&SRETRY=0 Abstract]] [[http://www3.interscience.wiley.com/cgi-bin/fulltext/112279243/PDFSTART Full Text]]<br />[http://www3.interscience.wiley.com/cgi-bin/jhome/34201 Bioessays], 2006, Vol28(2): 199-210.<br />
 
*Ontologies for data and knowledge sharing in biology: plant ROS signaling as a case study. [[http://www3.interscience.wiley.com/cgi-bin/abstract/112279243/ABSTRACT?CRETRY=1&SRETRY=0 Abstract]] [[http://www3.interscience.wiley.com/cgi-bin/fulltext/112279243/PDFSTART Full Text]]<br />[http://www3.interscience.wiley.com/cgi-bin/jhome/34201 Bioessays], 2006, Vol28(2): 199-210.<br />
  
−
 
+
*Pujar et al, 2006.'''Whole-plant growth stage ontology for angiosperms and its application in plant biology.''' [[http://www.plantphysiol.org/cgi/content/abstract/142/2/414 Abstract]] [[http://www.plantphysiol.org/cgi/content/full/142/2/414 Full Text]]<br />[http://www.plantphysiol.org/ Plant Physiology], 2006, 142: 414-428
  
 
==2005==
 
==2005==
 
*An ontology for cell types. [[http://genomebiology.com/2005/6/2/R21/abstract/ Abstract]] [[http://genomebiology.com/2005/6/2/R21 Full Text]]<br />[http://genomebiology.com/ Genome Biology], 2005, Vol 6: R21.<br />
 
*An ontology for cell types. [[http://genomebiology.com/2005/6/2/R21/abstract/ Abstract]] [[http://genomebiology.com/2005/6/2/R21 Full Text]]<br />[http://genomebiology.com/ Genome Biology], 2005, Vol 6: R21.<br />
 +
 +
*'''Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages.''' [[http://www.hindawi.com/GetArticle.aspx?doi=10.1002/cfg.496&e=CTA Abstract]] [[http://www.hindawi.com/GetPDF.aspx?doi=10.1002/cfg.496 Full Text]]<br />[http://www3.interscience.wiley.com/cgi-bin/jhome/77002016 Comparative and Functional Genomics], 2005, Volume 6(7-8), 388 - 397
  
 
*Relations in Biomedical Ontologies”, Genome Biology (2005), 6 (5), R46. [[http://genomebiology.com/2005/6/5/R46 Smith etal, 2005]]
 
*Relations in Biomedical Ontologies”, Genome Biology (2005), 6 (5), R46. [[http://genomebiology.com/2005/6/5/R46 Smith etal, 2005]]
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*Bio-ontologies-fast and furious. [[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v22/n6/full/nbt0604-773.html Full Text]] <br />[http://www.nature.com/nbt/ Nature Biotechnology], 2004, Vol 22(6): 773-774.
 
*Bio-ontologies-fast and furious. [[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v22/n6/full/nbt0604-773.html Full Text]] <br />[http://www.nature.com/nbt/ Nature Biotechnology], 2004, Vol 22(6): 773-774.
−
 
−
*Functional annotation of the Arabidopsis genome using controlled vocabularies. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15173566 Abstract]] [[http://www.plantphysiol.org/cgi/content/full/135/2/745 Full Text]] <br />[http://www.plantphysiol.org/ Plant Physiology], 2004, Vol 135(2): 745-755.
 
−
 
−
*Ontologies in biology: design, applications and future challenges. [[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nrg/journal/v5/n3/abs/nrg1295_fs.html&dynoptions=doi1090299222 Abstract]] [[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nrg/journal/v5/n3/full/nrg1295_fs.html&filetype=pdf Full Text]] <br />[http://www.nature.com/reviews/ Nature Reviews Genetics] 2004, Vol 5(3): 213-222.
 
  
 
*Functional annotation of the Arabidopsis genome using controlled vocabularies. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15173566 Abstract]] [[http://www.plantphysiol.org/cgi/content/full/135/2/745 Full Text]] <br />[http://www.plantphysiol.org/ Plant Physiology], 2004, Vol 135(2): 745-755.
 
*Functional annotation of the Arabidopsis genome using controlled vocabularies. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15173566 Abstract]] [[http://www.plantphysiol.org/cgi/content/full/135/2/745 Full Text]] <br />[http://www.plantphysiol.org/ Plant Physiology], 2004, Vol 135(2): 745-755.
Line 53: Line 48:
  
 
*Ontologies: Formalising biological knowledge for bioinformatics. [[http://www3.interscience.wiley.com/cgi-bin/abstract/104524933/ABSTRACT Abstract]] [[http://www3.interscience.wiley.com/cgi-bin/fulltext/104524933/PDFSTART Full Text]] <br />[http://www3.interscience.wiley.com/cgi-bin/jhome/34201 Bioessays], 2003, Vol 25(5): 501-506.
 
*Ontologies: Formalising biological knowledge for bioinformatics. [[http://www3.interscience.wiley.com/cgi-bin/abstract/104524933/ABSTRACT Abstract]] [[http://www3.interscience.wiley.com/cgi-bin/fulltext/104524933/PDFSTART Full Text]] <br />[http://www3.interscience.wiley.com/cgi-bin/jhome/34201 Bioessays], 2003, Vol 25(5): 501-506.
 +
 +
*Zea mays ontology – a database of international terms<br /> Trends in Plant Science, 2003, 8(11): 517-520 [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14607095&dopt=Abstract Abstract]]
  
 
==2002==
 
==2002==
 
*Extension and Integration of the Gene Ontology (GO): Combining GO Vocabularies With External Vocabularies. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12466303&dopt=Abstract Abstract]] [[http://www.genome.org/cgi/content/full/12/12/1982 Full Text]] <br />[http://www.genome.org/ Genome research] 2002,12: 1982-1991.
 
*Extension and Integration of the Gene Ontology (GO): Combining GO Vocabularies With External Vocabularies. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12466303&dopt=Abstract Abstract]] [[http://www.genome.org/cgi/content/full/12/12/1982 Full Text]] <br />[http://www.genome.org/ Genome research] 2002,12: 1982-1991.
  
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*The Plant Ontology<sup>TM</sup> Consortium and Plant Ontologies [[http://www3.interscience.wiley.com/cgi-bin/abstract/91016119/START Abstract]] [[http://www3.interscience.wiley.com/cgi-bin/fulltext/91016119/HTMLSTART Full Text]] <br />[http://www3.interscience.wiley.com/cgi-bin/jtoc?Type=DD&ID=91016119 Comparative and Functional Genomics], 2002, Vol 3(2), 137-142.
+
'''*The Plant Ontology<sup>TM</sup> Consortium and Plant Ontologies''' [[http://www3.interscience.wiley.com/cgi-bin/abstract/91016119/START Abstract]] [[http://www3.interscience.wiley.com/cgi-bin/fulltext/91016119/HTMLSTART Full Text]] <br />[http://www3.interscience.wiley.com/cgi-bin/jtoc?Type=DD&ID=91016119 Comparative and Functional Genomics], 2002, Vol 3(2), 137-142.
  
 
*Gramene: development and integration of trait and gene ontologies for rice [[http://www3.interscience.wiley.com/cgi-bin/abstract/91016047/START Abstract]] [[http://www3.interscience.wiley.com/cgi-bin/fulltext/91016047/HTMLSTART Full Text]] <br />[http://www3.interscience.wiley.com/cgi-bin/jtoc?Type=DD&ID=91016119 Comparative and Functional Genomics], 2002, Vol 3(2), 132-136.
 
*Gramene: development and integration of trait and gene ontologies for rice [[http://www3.interscience.wiley.com/cgi-bin/abstract/91016047/START Abstract]] [[http://www3.interscience.wiley.com/cgi-bin/fulltext/91016047/HTMLSTART Full Text]] <br />[http://www3.interscience.wiley.com/cgi-bin/jtoc?Type=DD&ID=91016119 Comparative and Functional Genomics], 2002, Vol 3(2), 132-136.
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*On the representation of gene function in genetic databases. by Michael Ashburner, ISMB 1998. [[http://www.geneontology.org/doc/gene_ontology_discussion.html HTML]]
 
*On the representation of gene function in genetic databases. by Michael Ashburner, ISMB 1998. [[http://www.geneontology.org/doc/gene_ontology_discussion.html HTML]]
−
 
−
 
−
 
−
 
−
 
−
*Extension and Integration of the Gene Ontology (GO): Combining GO Vocabularies With External Vocabularies. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12466303&dopt=Abstract Abstract]] [[http://www.genome.org/cgi/content/full/12/12/1982 Full Text]] <br />[http://www.genome.org/ Genome research] 2002,12: 1982-1991.
 
−
 
−
*The Plant Ontology<sup>TM</sup> Consortium and Plant Ontologies [[http://www3.interscience.wiley.com/cgi-bin/abstract/91016119/START Abstract]] [[http://www3.interscience.wiley.com/cgi-bin/fulltext/91016119/HTMLSTART Full Text]] <br />[http://www3.interscience.wiley.com/cgi-bin/jtoc?Type=DD&ID=91016119 Comparative and Functional Genomics], 2002, Vol 3(2), 137-142
 
−
 
−
*Gramene: development and integration of trait and gene ontologies for rice [[http://www3.interscience.wiley.com/cgi-bin/abstract/91016047/START Abstract]] [[http://www3.interscience.wiley.com/cgi-bin/fulltext/91016047/HTMLSTART Full Text]] <br />[http://www3.interscience.wiley.com/cgi-bin/jtoc?Type=DD&ID=91016119 Comparative and Functional Genomics], 2002, Vol 3(2), 132-136
 
−
 
−
*Creating the gene ontology resource: design and implementation. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11483584&dopt=Abstract Abstract]] [[http://www.genome.org/cgi/content/full/11/8/1425 Full Text]] <br />[http://www.genome.org/ Genome Research], 2001, Vol 11(8), 1425-1433
 
−
 
−
*Gene Ontology: tool for the unification of biology. [[http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10802651&dopt=Abstract Abstract]] [[http://www.nature.com/cgi-taf/DynaPage.taf?file=/ng/journal/v25/n1/full/ng0500_25.html Full Text]] <br />[http://www.nature.com/ng/ Nature Genetics], 2000, 25: 25-29
 
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*On the representation of gene function in genetic databases. by Michael Ashburner, ISMB 1998. [[http://www.geneontology.org/doc/gene_ontology_discussion.html HTML]] <br />
 
−
 
−
Publications
 
−
 
−
Plant Structure Ontology (PSO) - A morphological and anatomical ontology of flowering plants. In Anatomy Ontologies for Bioinformatics, Springer, 2008, p 27-42. [Book]
 
−
 
−
The Plant Ontology Database: a community resource for plant structure and development stages controlled vocabulary and annotations.  [Abstract]  [Full Text]
 
−
Nucleic Acid Research, 2008, 36(Database issue):D449-D454
 
−
 
−
The Plant Structure Ontology, a unified vocabulary of anatomy and morphology of a flowering plant.    [Abstract]  [Full Text]
 
−
Plant Physiology, 2007, 143: 587-599 
 
−
 
−
Whole-plant growth stage ontology for angiosperms and its application in plant biology.  [Abstract]  [Full Text]
 
−
Plant Physiology, 2006, 142: 414-428
 
−
 
−
Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages.  [Abstract]  [Full Text]
 
−
Comparative and Functional Genomics, 2005, Volume 6(7-8), 388 - 397
 
−
 
−
The Gene Ontology (GO) database and informatics resource.  [Abstract]  [Full Text]
 
−
Nucleic Acids Research, 2004, Vol 32: D258-D261.
 
−
 
−
Bio-ontologies-fast and furious.  [Full Text]
 
−
Nature Biotechnology, 2004, Vol 22(6): 773-774.
 
−
 
−
Functional annotation of the Arabidopsis genome using controlled vocabularies.  [Abstract]  [Full Text]
 
−
Plant Physiology, 2004, Vol 135(2): 745-755.
 
−
 
−
Ontologies in biology: design, applications and future challenges.    [Abstract]  [Full Text]
 
−
Nature Reviews Genetics 2004, Vol 5(3): 213-222.
 
−
 
−
Zea mays ontology – a database of international terms
 
−
Trends in Plant Science, 2003, 8(11): 517-520 [Abstract]
 
−
 
−
Ontologies: Formalising biological knowledge for bioinformatics.  [Abstract]  [Full Text]
 
−
Bioessays, 2003, Vol 25(5): 501-506.
 
−
 
−
Extension and Integration of the Gene Ontology (GO): Combining GO Vocabularies With External Vocabularies.    [Abstract]  [Full Text]
 
−
Genome research 2002,12: 1982-1991.
 
−
 
−
The Plant OntologyTM Consortium and Plant Ontologies  [Abstract]  [Full Text]
 
−
Comparative and Functional Genomics, 2002, Vol 3(2), 137-142
 
−
 
−
Gramene: development and integration of trait and gene ontologies for rice  [Abstract]  [Full Text]
 
−
Comparative and Functional Genomics, 2002, Vol 3(2), 132-136
 
−
 
−
Creating the gene ontology resource: design and implementation.  [Abstract]  [Full Text]
 
−
Genome Research, 2001, Vol 11(8), 1425-1433
 
−
 
−
Gene Ontology: tool for the unification of biology.  [Abstract]  [Full Text]
 
−
Nature Genetics, 2000, 25: 25-29
 
−
 
−
On the representation of gene function in genetic databases. by Michael Ashburner, ISMB 1998.  [HTML]
 
−
 
−
[[Category:Documents]]
 
−
[[Category:Publications]]
 

Latest revision as of 00:43, 13 July 2014

2013

2012

  • Lens et al. 2012. An extension of the Plant Ontology project supporting wood anatomy and development research. IAWA Journal 33: 113–117.
  • Arnaud, et al (2012). Towards a Reference Plant Trait Ontology for Modeling Knowledge of Plant Traits and Phenotypes. Proceedings of the International Conference on Knowledge Engineering and Ontology Development. Barcelona, Spain, pp 220–225
  • Walls et al (2012). Ontologies as integrative tools for plant science. American Journal of Botany 99: 1263 –1275 (special invited paper).

2008

  • Ilic et al, 2008. Plant Structure Ontology (PSO) - A morphological and anatomical ontology of flowering plants. In Anatomy Ontologies for Bioinformatics, Springer, p 27-42. Book
  • Avraham et al, 2008.The Plant Ontology Database: a community resource for plant structure and development stages controlled vocabulary and annotations. Abstract Full Text]
    Nucleic Acid Research, 36(Database issue):D449-D454

2007

  • The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration”, Nature Biotechnology,25 (11), November 2007, 1251 -1255. [Smith et al, 2007]
  • Ilic et al, 2007.The Plant Structure Ontology, a unified vocabulary of anatomy and morphology of a flowering plant. [Abstract] [Full Text]
    Plant Physiology, 2007, 143: 587-599

2006

  • Ontologies for data and knowledge sharing in biology: plant ROS signaling as a case study. [Abstract] [Full Text]
    Bioessays, 2006, Vol28(2): 199-210.

2005

  • Relations in Biomedical Ontologies”, Genome Biology (2005), 6 (5), R46. [Smith etal, 2005]

2004

2003

  • Zea mays ontology – a database of international terms
    Trends in Plant Science, 2003, 8(11): 517-520 [Abstract]

2002

  • Extension and Integration of the Gene Ontology (GO): Combining GO Vocabularies With External Vocabularies. [Abstract] [Full Text]
    Genome research 2002,12: 1982-1991.

*The Plant OntologyTM Consortium and Plant Ontologies [Abstract] [Full Text]
Comparative and Functional Genomics, 2002, Vol 3(2), 137-142.

  • Surrounding Space: On the Ontology of Organism-Environment Relations. Theory in Biosciences 120:2 (2002), 139–162 [Smith and Varzi, 2002]

2001

2000 and Older

  • On the representation of gene function in genetic databases. by Michael Ashburner, ISMB 1998. [HTML]
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