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| − | * '''Try the Beta version of the [http://kb.phenoscape.org Phenoscape Knowledgebase].''' Development is very much in progress, and your feedback is welcome! | + | * Try the [http://kb.phenoscape.org Phenoscape Knowledgebase]. Your feedback is welcome! |
| − | * Check out the latest news on the [http://blog.phenoscape.org/ Phenoscape blog], including the latest changes to PATO, a new bridging Vertebrate Anatomy Ontology, and the launch of a new Phenotype Ontology Research Coordination Network. | + | * Check out the latest news on the [http://blog.phenoscape.org/ Phenoscape blog] |
| − | * Recent publications:
| + | * Learn more in one of our upcoming [[Training_and_Workshops | training workshops]] |
| − | ** [http://sysbio.oxfordjournals.org/content/59/4/369.full "The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age"] was published in the July 2010 issue of Systematic Biology; see our ontology [http://sysbio.oxfordjournals.org/content/vol59/issue4/cover.dtl cover art] that was selected for this issue! | |
| − | ** [http://dx.plos.org/10.1371/journal.pone.0010708 “Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature”] was published in PLoS ONE in May 2010.
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| − | ** [http://dx.plos.org/10.1371/journal.pone.0010500 “Phenex: Ontological Annotation of Phenotypic Diversity”] was published in PLoS ONE in May 2010. Download [http://blog.phenoscape.org/2009/11/25/phenex-1-0/ Phenex 1.0] here.
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| − | ==Linking Evolution to Genomics Using Phenotype Ontologies== | + | == Enabling Machine-actionable Semantics for Comparative Analysis of Trait Evolution == |
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| − | [[Image:NESCent Logo.png|right]]
| + | The current project of the Phenoscape team is Enabling Machine-actionable '''S'''emantics for '''C'''omparative '''A'''nalysis of '''T'''rait '''E'''volution (SCATE). |
| − | ===About this project===
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| − | What are the developmental and genetic bases of evolutionary differences in morphology across species? Currently it is difficult to approach this question due to a lack of computational tools that allow researchers to integrate developmental genetic and comparative morphological/anatomical data.
| + | The objective is to create infrastructure that will provide comparative trait analysis tools easy access to algorithms powered by machine reasoning with the semantics of trait descriptions. Similar to how Google, IBM Watson, and others have enabled developers of smartphone apps to incorporate, with only a few lines of code, complex machine-learning and artificial intelligence capabilities such as sentiment analysis, we aim to demonstrate how easy access to knowledge computing opens up new opportunities for analysis, tools, and research in comparative trait analysis. |
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| − | [[Image:Ctol Logo.jpg|right]] [[Image:Zfinlogo.png|left]] We are addressing this by developing a database of evolutionarily variable morphological characters for a large clade of fishes (the Ostariophysi) and connecting this database to the large collection of mutant phenotypes in the [http://zfin.org ZFIN database], the central database of the zebrafish model organism community. The evolutionary and mutant phenotypes are being described using common [[#The_Role_of_Ontologies|ontologies]]. The database with its web-interface, together with the extended ontologies and data curation tools, will allow researchers to ask novel questions about the genetic and developmental regulation of evolutionary morphological transitions. Tool and database development are being guided by [http://en.wikipedia.org/wiki/Use_case use cases], or driving research questions, defined by the devo-evo community. These tools are being developed under an open-source, open-development model, and in such a way that they can be used for additional biological systems in the future.
| + | As driving biological research questions, we focus on addressing three long-standing limitations in comparative studies of trait evolution: recombining trait data, modeling trait evolution, and generating testable hypotheses for the drivers of trait adaptation. |
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| − | [[Image:Deepfin Logo.gif|right]] This project is a unique collaboration between evolutionary and model organism biologists including two national centers ([http://www.nescent.org NESCent] and [http://www.bioontology.org NCBO]), the [http://zfin.org ZFIN model organism database], the [http://bio.slu.edu/mayden/cypriniformes/home.html Cypriniformes Tree of Life] project, the [http://www.deepfin.org/ DeepFin Research Coordination Network], and the morphological image databases used by the evolutionary biology community.
| + | SCATE is funded by NSF collaborative grants DBI-1661456 (Duke University), DBI-1661529 (Virginia Tech), DBI-1661516 (University of South Dakota), and DBI-1661356 (UNC Chapel Hill and RENCI) from Sep 1, 2017 to Aug 31, 2020. |
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| − | ===The Role of Ontologies===
| + | The grant proposal text with references is publicly available: ''W. Dahdul, J.P. Balhoff, H. Lapp, P. M. Mabee, J. Uyeda, & T.J. Vision. (2017). Enabling machine-actionable semantics for comparative analyses of trait evolution. Zenodo. http://doi.org/10.5281/zenodo.885538''. |
| − | [[Image:Ncbo logo.gif|right]]
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| − | ====Background====
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| − | Ontologies are constrained, structured vocabularies with well defined relationships among terms. Ontologies represent the knowledge of a particular discipline and provide not only a mechanism for consistent annotation of data, but also greater interoperability among people and machines. The most widely used biological ontology is the [http://www.geneontology.org Gene Ontology], which is utilized to annotate molecular function, biological processes and subcellular localization to gene products from different organisms.
| + | See the [http://scate.phenoscape.org project website] for more information. For a little more background on the how and why of incorporating ontologies into comparative analysis, see [[ComparativeAnalysis]]. |
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| − | ====Phenotype ontologies==== | + | == Previous Phenoscape projects and Acknowledgements == |
| | + | * Phenoscape II ("[[Ontology-enabled reasoning across phenotypes from evolution and model organisms]]") was funded by NSF collaborative grants DBI-1062404 and DBI-1062542 from July 1, 2011, to June 30, 2018, and supported by the National Evolutionary Synthesis Center (NESCent), NSF #EF-0905606. The original Project Description for this grant is available [[:File:Phenoscape_Project_description_refs.pdf| here]]. |
| | + | * Phenoscape I ("[[Linking Evolution to Genomics Using Phenotype Ontologies]]") was funded by NSF grant BDI-0641025 from June 1, 2007, to Jun 30, 2011, and was supported by NESCent, NSF #EF-0423641. |
| | + | * The original ideas for Phenoscape arose from a NESCent <span class="plainlinks">[http://www.nescent.org/science/workinggroup.php Working Group]</span> led by Paula Mabee and Monte Westerfield, "[[Fish Evolution Working Group|Towards an Integrated Database for Fish Evolution]]." |
| | + | * These projects have bene made possible possible by the hard work of [[Acknowledgments#Contributors| numerous contributors]]. |
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| − | [[Image:EAV4_layers_flat2.png|right|320px]] Approximately 500 mutant zebrafish lines (alleles) with over 660 annotated phenotypic characters from the jaw or gill arches, fins, axial skeleton and other features of the skeleton have been described. Curators in the [http://www.zfin.org Zebrafish Information Network] (ZFIN) are annotating mutant phenotypes using the [http://obofoundry.org/cgi-bin/detail.cgi?id=zebrafish_anatomy&title=Zebrafish%20anatomy%20and%20development zebrafish anatomy ontology] and the [http://www.bioontology.org/wiki/index.php/PATO:Main_Page Phenotype And Trait Ontology] (PATO). PATO is a “universal” ontology of terms describing qualities (e.g. shape, color, size) that may be applied to any organism.
| + | https://www.nescent.org/about/images/nsf_logo.jpg |
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| − | ====Anatomical ontologies====
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| − | We have initiated a multi-species ontology for ostariophysan fishes, the [[Teleost Anatomy Ontology]] (TAO), which was initialized with the terms in the zebrafish anatomical ontology. The development of the TAO is currently focused on the skeletal system because it varies significantly across the Ostariophysi, is well-preserved in fossil specimens, and it is often the focus of morphologically-based evolutionary studies in ichthyology.
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| − | This multi-species anatomy ontology is being used in combination with the PATO ontology (see EQ format) to describe the comparative morphological characters. We have also developed a separate catalog of homology statements for entities within the TAO, so that individual investigators may select particular relationships based on evidence.
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| − | ====Taxonomic ontology====
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| − | Together with taxonomic experts, we have developed a taxonomic ontology (based on the [http://www.calacademy.org/RESEARCH/ichthyology/catalog/fishcatsearch.html Catalog of Fishes]) to relate species with particular characters and states. The taxonomic ontology will include nodes ancestral to the Ostariophysi as far back as the Vertebrata in order to associate certain anatomical terms with more inclusive clades than the Ostariophysi.
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| − | ====Fish Morphology====
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| − | Although the comparative anatomy of fishes has been documented in the literature for several hundred years, it is not available in a computable format. With the help of taxon experts for ostariophysan fishes, we prioritized 76 papers for curation; these can be viewed on our publicly available [http://spreadsheets.google.com/ccc?key=pTeXfTnVPxC-P1URVHbI4Qg Google spreadsheet]. 51 have been completely curated and consistency checked and are available for searching in the Knowledgebase. We achieved our goal to input approximately 5,000 morphological features in an “EQ” format ([[Media:TREE Mabee.pdf|Mabee et al. 2007a]]<!--; Mabee et al. 2007 in process-->) http://dx.plos.org/10.1371/journal.pone.0010708 using a combination of ontologies.
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| − | ===Contact===
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| − | Paula Mabee (University of South Dakota) is the Principal Investigator. Co-principal investigators are Todd Vision (University of North Carolina, Chapel Hill), Monte Westerfield (University of Oregon, ZFIN), and Hilmar Lapp (NESCent) ([[Contact|see their contact addresses]]).
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| − | ==Acknowledgments==
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| − | {|
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| − | | This project is funded by NSF grant BDI<nowiki>-</nowiki>0641025, and supported by the National Evolutionary Synthesis Center (NESCent), NSF #EF-0423641. <br/><br/>This project arose from a NESCent <span class="plainlinks">[http://www.nescent.org/science/workinggroup.php Working Group]</span> led by Paula Mabee and Monte Westerfield, "Towards an Integrated Database for Fish Evolution." [[Fish Evolution Working Group|Goals and summaries of the group]] are archived on this wiki.
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| − | | http://www.nescent.org/about/images/nsf_logo.jpg
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| − | |}
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| − | ==Pages of public interest==
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| − | * [[Training and Workshops]]
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Enabling Machine-actionable Semantics for Comparative Analysis of Trait Evolution
The current project of the Phenoscape team is Enabling Machine-actionable Semantics for Comparative Analysis of Trait Evolution (SCATE).
The objective is to create infrastructure that will provide comparative trait analysis tools easy access to algorithms powered by machine reasoning with the semantics of trait descriptions. Similar to how Google, IBM Watson, and others have enabled developers of smartphone apps to incorporate, with only a few lines of code, complex machine-learning and artificial intelligence capabilities such as sentiment analysis, we aim to demonstrate how easy access to knowledge computing opens up new opportunities for analysis, tools, and research in comparative trait analysis.
As driving biological research questions, we focus on addressing three long-standing limitations in comparative studies of trait evolution: recombining trait data, modeling trait evolution, and generating testable hypotheses for the drivers of trait adaptation.
SCATE is funded by NSF collaborative grants DBI-1661456 (Duke University), DBI-1661529 (Virginia Tech), DBI-1661516 (University of South Dakota), and DBI-1661356 (UNC Chapel Hill and RENCI) from Sep 1, 2017 to Aug 31, 2020.
The grant proposal text with references is publicly available: W. Dahdul, J.P. Balhoff, H. Lapp, P. M. Mabee, J. Uyeda, & T.J. Vision. (2017). Enabling machine-actionable semantics for comparative analyses of trait evolution. Zenodo. http://doi.org/10.5281/zenodo.885538.
See the project website for more information. For a little more background on the how and why of incorporating ontologies into comparative analysis, see ComparativeAnalysis.
Previous Phenoscape projects and Acknowledgements
- Phenoscape II ("Ontology-enabled reasoning across phenotypes from evolution and model organisms") was funded by NSF collaborative grants DBI-1062404 and DBI-1062542 from July 1, 2011, to June 30, 2018, and supported by the National Evolutionary Synthesis Center (NESCent), NSF #EF-0905606. The original Project Description for this grant is available here.
- Phenoscape I ("Linking Evolution to Genomics Using Phenotype Ontologies") was funded by NSF grant BDI-0641025 from June 1, 2007, to Jun 30, 2011, and was supported by NESCent, NSF #EF-0423641.
- The original ideas for Phenoscape arose from a NESCent Working Group led by Paula Mabee and Monte Westerfield, "Towards an Integrated Database for Fish Evolution."
- These projects have bene made possible possible by the hard work of numerous contributors.
