The Experts below are selected from a list of 2448 Experts worldwide ranked by ideXlab platform

Christopher J Mungall - One of the best experts on this subject based on the ideXlab platform.

  • the porifera Ontology poro enhancing sponge systematics with an Anatomy Ontology
    Journal of Biomedical Semantics, 2014
    Co-Authors: Robert W Thacker, Melissa A Haendel, Adeline Kerner, Erik Segerdell, Maria Diaz, Regine Vigneslebbe, Christopher J Mungall
    Abstract:

    Porifera (sponges) are ancient basal metazoans that lack organs. They provide insight into key evolutionary transitions, such as the emergence of multicellularity and the nervous system. In addition, their ability to synthesize unusual compounds offers potential biotechnical applications. However, much of the knowledge of these organisms has not previously been codified in a machine-readable way using modern web standards. The Porifera Ontology is intended as a standardized coding system for sponge anatomical features currently used in systematics. The Ontology is available from http://purl.obolibrary.org/obo/poro.owl , or from the project homepage http://porifera-Ontology.googlecode.com/ . The version referred to in this manuscript is permanently available from http://purl.obolibrary.org/obo/poro/releases/2014-03-06/ . By standardizing character representations, we hope to facilitate more rapid description and identification of sponge taxa, to allow integration with other evolutionary database systems, and to perform character mapping across the major clades of sponges to better understand the evolution of morphological features. Future applications of the Ontology will focus on creating (1) Ontology-based species descriptions; (2) taxonomic keys that use the nested terms of the Ontology to more quickly facilitate species identifications; and (3) methods to map anatomical characters onto molecular phylogenies of sponges. In addition to modern taxa, the Ontology is being extended to include features of fossil taxa.

  • The Porifera Ontology (PORO): enhancing sponge systematics with an Anatomy Ontology
    Journal of Biomedical Semantics, 2014
    Co-Authors: Robert W Thacker, Melissa A Haendel, Maria Cristina Díaz, Adeline Kerner, Régine Vignes-lebbe, Erik Segerdell, Christopher J Mungall
    Abstract:

    Background Porifera (sponges) are ancient basal metazoans that lack organs. They provide insight into key evolutionary transitions, such as the emergence of multicellularity and the nervous system. In addition, their ability to synthesize unusual compounds offers potential biotechnical applications. However, much of the knowledge of these organisms has not previously been codified in a machine-readable way using modern web standards. Results The Porifera Ontology is intended as a standardized coding system for sponge anatomical features currently used in systematics. The Ontology is available from http://purl.obolibrary.org/obo/poro.owl , or from the project homepage http://porifera-Ontology.googlecode.com/ . The version referred to in this manuscript is permanently available from http://purl.obolibrary.org/obo/poro/releases/2014-03-06/ . Conclusions By standardizing character representations, we hope to facilitate more rapid description and identification of sponge taxa, to allow integration with other evolutionary database systems, and to perform character mapping across the major clades of sponges to better understand the evolution of morphological features. Future applications of the Ontology will focus on creating (1) Ontology-based species descriptions; (2) taxonomic keys that use the nested terms of the Ontology to more quickly facilitate species identifications; and (3) methods to map anatomical characters onto molecular phylogenies of sponges. In addition to modern taxa, the Ontology is being extended to include features of fossil taxa.

  • Computing on the anatomical form for disease discovery (338.1)
    The FASEB Journal, 2014
    Co-Authors: Melissa A Haendel, Christopher J Mungall
    Abstract:

    Elucidating evolutionary processes, disease, and developmental dysfunction requires understanding variation in phenotype. However, anatomical information, integration, and retrieval are key challenges as reference to Anatomy is largely unstructured or encoded in a variety of formats. An Ontology is useful to annotate, link, and retrieve anatomical data, and can be computed on using a reasoner. The use of Anatomy ontologies provides a new mechanism on which to base a systems biology approach to understanding phenotypic diversity and dysmorphology. Here, we present our efforts as part of the Monarch Initiative to support the identification of relevant genes linked to human diseases. Towards this end, we constructed the Uberon multi-species Anatomy Ontology to provide generalization and links between anatomical structures in model organisms. Use of Uberon with other modular ontologies, such as the Biological Spatial Ontology (BSPO) to record spatial and topological relationships among biological structures, ...

  • The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments
    Journal of biomedical semantics, 2013
    Co-Authors: Paola Roncaglia, Maryann E. Martone, D. P. Hill, Tanya Z. Berardini, Rebecca E. Foulger, Fahim T. Imam, H. Drabkin, Christopher J Mungall, Jane Lomax
    Abstract:

    Background The Gene Ontology (GO) (http://www.geneOntology.org/) contains a set of terms for describing the activity and actions of gene products across all kingdoms of life. Each of these activities is executed in a location within a cell or in the vicinity of a cell. In order to capture this context, the GO includes a sub-Ontology called the Cellular Component (CC) Ontology (GO-CCO). The primary use of this Ontology is for GO annotation, but it has also been used for phenotype annotation, and for the annotation of images. Another Ontology with similar scope to the GO-CCO is the Subcellular Anatomy Ontology (SAO), part of the Neuroscience Information Framework Standard (NIFSTD) suite of ontologies. The SAO also covers cell components, but in the domain of neuroscience.

  • The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments
    Journal of Biomedical Semantics, 2013
    Co-Authors: Paola Roncaglia, Maryann E. Martone, D. P. Hill, Tanya Z. Berardini, Rebecca E. Foulger, Fahim T. Imam, H. Drabkin, Christopher J Mungall, Jane Lomax
    Abstract:

    Background The Gene Ontology (GO) ( http://www.geneOntology.org/ ) contains a set of terms for describing the activity and actions of gene products across all kingdoms of life. Each of these activities is executed in a location within a cell or in the vicinity of a cell. In order to capture this context, the GO includes a sub-Ontology called the Cellular Component (CC) Ontology (GO-CCO). The primary use of this Ontology is for GO annotation, but it has also been used for phenotype annotation, and for the annotation of images. Another Ontology with similar scope to the GO-CCO is the Subcellular Anatomy Ontology (SAO), part of the Neuroscience Information Framework Standard (NIFSTD) suite of ontologies. The SAO also covers cell components, but in the domain of neuroscience. Description Recently, the GO-CCO was enriched in content and links to the Biological Process and Molecular Function branches of GO as well as to other ontologies. This was achieved in several ways. We carried out an amalgamation of SAO terms with GO-CCO ones; as a result, nearly 100 new neuroscience-related terms were added to the GO. The GO-CCO also contains relationships to GO Biological Process and Molecular Function terms, as well as connecting to external ontologies such as the Cell Ontology (CL). Terms representing protein complexes in the Protein Ontology (PRO) reference GO-CCO terms for their species-generic counterparts. GO-CCO terms can also be used to search a variety of databases. Conclusions In this publication we provide an overview of the GO-CCO, its overall design, and some recent extensions that make use of additional spatial information. One of the most recent developments of the GO-CCO was the merging in of the SAO, resulting in a single unified Ontology designed to serve the needs of GO annotators as well as the specific needs of the neuroscience community.

Melissa A Haendel - One of the best experts on this subject based on the ideXlab platform.

  • The Porifera Ontology (PORO): enhancing sponge systematics with an Anatomy Ontology
    Journal of Biomedical Semantics, 2014
    Co-Authors: Robert W Thacker, Melissa A Haendel, Maria Cristina Díaz, Adeline Kerner, Régine Vignes-lebbe, Erik Segerdell, Christopher J Mungall
    Abstract:

    Background Porifera (sponges) are ancient basal metazoans that lack organs. They provide insight into key evolutionary transitions, such as the emergence of multicellularity and the nervous system. In addition, their ability to synthesize unusual compounds offers potential biotechnical applications. However, much of the knowledge of these organisms has not previously been codified in a machine-readable way using modern web standards. Results The Porifera Ontology is intended as a standardized coding system for sponge anatomical features currently used in systematics. The Ontology is available from http://purl.obolibrary.org/obo/poro.owl , or from the project homepage http://porifera-Ontology.googlecode.com/ . The version referred to in this manuscript is permanently available from http://purl.obolibrary.org/obo/poro/releases/2014-03-06/ . Conclusions By standardizing character representations, we hope to facilitate more rapid description and identification of sponge taxa, to allow integration with other evolutionary database systems, and to perform character mapping across the major clades of sponges to better understand the evolution of morphological features. Future applications of the Ontology will focus on creating (1) Ontology-based species descriptions; (2) taxonomic keys that use the nested terms of the Ontology to more quickly facilitate species identifications; and (3) methods to map anatomical characters onto molecular phylogenies of sponges. In addition to modern taxa, the Ontology is being extended to include features of fossil taxa.

  • the porifera Ontology poro enhancing sponge systematics with an Anatomy Ontology
    Journal of Biomedical Semantics, 2014
    Co-Authors: Robert W Thacker, Melissa A Haendel, Adeline Kerner, Erik Segerdell, Maria Diaz, Regine Vigneslebbe, Christopher J Mungall
    Abstract:

    Porifera (sponges) are ancient basal metazoans that lack organs. They provide insight into key evolutionary transitions, such as the emergence of multicellularity and the nervous system. In addition, their ability to synthesize unusual compounds offers potential biotechnical applications. However, much of the knowledge of these organisms has not previously been codified in a machine-readable way using modern web standards. The Porifera Ontology is intended as a standardized coding system for sponge anatomical features currently used in systematics. The Ontology is available from http://purl.obolibrary.org/obo/poro.owl , or from the project homepage http://porifera-Ontology.googlecode.com/ . The version referred to in this manuscript is permanently available from http://purl.obolibrary.org/obo/poro/releases/2014-03-06/ . By standardizing character representations, we hope to facilitate more rapid description and identification of sponge taxa, to allow integration with other evolutionary database systems, and to perform character mapping across the major clades of sponges to better understand the evolution of morphological features. Future applications of the Ontology will focus on creating (1) Ontology-based species descriptions; (2) taxonomic keys that use the nested terms of the Ontology to more quickly facilitate species identifications; and (3) methods to map anatomical characters onto molecular phylogenies of sponges. In addition to modern taxa, the Ontology is being extended to include features of fossil taxa.

  • Computing on the anatomical form for disease discovery (338.1)
    The FASEB Journal, 2014
    Co-Authors: Melissa A Haendel, Christopher J Mungall
    Abstract:

    Elucidating evolutionary processes, disease, and developmental dysfunction requires understanding variation in phenotype. However, anatomical information, integration, and retrieval are key challenges as reference to Anatomy is largely unstructured or encoded in a variety of formats. An Ontology is useful to annotate, link, and retrieve anatomical data, and can be computed on using a reasoner. The use of Anatomy ontologies provides a new mechanism on which to base a systems biology approach to understanding phenotypic diversity and dysmorphology. Here, we present our efforts as part of the Monarch Initiative to support the identification of relevant genes linked to human diseases. Towards this end, we constructed the Uberon multi-species Anatomy Ontology to provide generalization and links between anatomical structures in model organisms. Use of Uberon with other modular ontologies, such as the Biological Spatial Ontology (BSPO) to record spatial and topological relationships among biological structures, ...

  • The zebrafish Anatomy and stage ontologies: representing the Anatomy and development of Danio rerio
    Journal of Biomedical Semantics, 2014
    Co-Authors: Ceri E Van Slyke, Monte Westerfield, Yvonne M Bradford, Melissa A Haendel
    Abstract:

    Background The Zebrafish Anatomy Ontology (ZFA) is an OBO Foundry Ontology that is used in conjunction with the Zebrafish Stage Ontology (ZFS) to describe the gross and cellular Anatomy and development of the zebrafish, Danio rerio , from single cell zygote to adult. The zebrafish model organism database (ZFIN) uses the ZFA and ZFS to annotate phenotype and gene expression data from the primary literature and from contributed data sets. Results The ZFA models Anatomy and development with a subclass hierarchy, a partonomy, and a developmental hierarchy and with relationships to the ZFS that define the stages during which each anatomical entity exists. The ZFA and ZFS are developed utilizing OBO Foundry principles to ensure orthogonality, accessibility, and interoperability. The ZFA has 2860 classes representing a diversity of anatomical structures from different anatomical systems and from different stages of development. Conclusions The ZFA describes zebrafish Anatomy and development semantically for the purposes of annotating gene expression and anatomical phenotypes. The Ontology and the data have been used by other resources to perform cross-species queries of gene expression and phenotype data, providing insights into genetic relationships, morphological evolution, and models of human disease.

  • The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age
    Systematic biology, 2010
    Co-Authors: Wasila M Dahdul, Monte Westerfield, James P Balhoff, Hilmar Lapp, John G Lundberg, Peter E. Midford, Melissa A Haendel, Paula M Mabee
    Abstract:

    The rich knowledge of morphological variation among organisms reported in the systematic literature has remained in free-text format, impractical for use in large-scale synthetic phylogenetic work. This noncomputable format has also precluded linkage to the large knowledgebase of genomic, genetic, developmental, and phenotype data in model organism databases. We have undertaken an effort to prototype a curated, Ontology-based evolutionary morphology database that maps to these genetic databases (http://kb.phenoscape.org) to facilitate investigation into the mechanistic basis and evolution of phenotypic diversity. Among the first requirements in establishing this database was the development of a multispecies Anatomy Ontology with the goal of capturing anatomical data in a systematic and computable manner. An Ontology is a formal representation of a set of concepts with defined relationships between those concepts. Multispecies Anatomy ontologies in particular are an efficient way to represent the diversity of morphological structures in a clade of organisms, but they present challenges in their development relative to single-species Anatomy ontologies. Here, we describe the Teleost Anatomy Ontology (TAO), a multispecies Anatomy Ontology for teleost fishes derived from the Zebrafish Anatomical Ontology (ZFA) for the purpose of annotating varying morphological features across species. To facilitate interoperability with other Anatomy ontologies, TAO uses the Common Anatomy Reference Ontology as a template for its upper level nodes, and TAO and ZFA are synchronized, with zebrafish terms specified as subtypes of teleost terms. We found that the details of Ontology architecture have ramifications for querying, and we present general challenges in developing a multispecies Anatomy Ontology, including refinement of definitions, taxon-specific relationships among terms, and representation of taxonomically variable developmental pathways.

Jane Lomax - One of the best experts on this subject based on the ideXlab platform.

  • The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments
    Journal of biomedical semantics, 2013
    Co-Authors: Paola Roncaglia, Maryann E. Martone, D. P. Hill, Tanya Z. Berardini, Rebecca E. Foulger, Fahim T. Imam, H. Drabkin, Christopher J Mungall, Jane Lomax
    Abstract:

    Background The Gene Ontology (GO) (http://www.geneOntology.org/) contains a set of terms for describing the activity and actions of gene products across all kingdoms of life. Each of these activities is executed in a location within a cell or in the vicinity of a cell. In order to capture this context, the GO includes a sub-Ontology called the Cellular Component (CC) Ontology (GO-CCO). The primary use of this Ontology is for GO annotation, but it has also been used for phenotype annotation, and for the annotation of images. Another Ontology with similar scope to the GO-CCO is the Subcellular Anatomy Ontology (SAO), part of the Neuroscience Information Framework Standard (NIFSTD) suite of ontologies. The SAO also covers cell components, but in the domain of neuroscience.

  • The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments
    Journal of Biomedical Semantics, 2013
    Co-Authors: Paola Roncaglia, Maryann E. Martone, D. P. Hill, Tanya Z. Berardini, Rebecca E. Foulger, Fahim T. Imam, H. Drabkin, Christopher J Mungall, Jane Lomax
    Abstract:

    Background The Gene Ontology (GO) ( http://www.geneOntology.org/ ) contains a set of terms for describing the activity and actions of gene products across all kingdoms of life. Each of these activities is executed in a location within a cell or in the vicinity of a cell. In order to capture this context, the GO includes a sub-Ontology called the Cellular Component (CC) Ontology (GO-CCO). The primary use of this Ontology is for GO annotation, but it has also been used for phenotype annotation, and for the annotation of images. Another Ontology with similar scope to the GO-CCO is the Subcellular Anatomy Ontology (SAO), part of the Neuroscience Information Framework Standard (NIFSTD) suite of ontologies. The SAO also covers cell components, but in the domain of neuroscience. Description Recently, the GO-CCO was enriched in content and links to the Biological Process and Molecular Function branches of GO as well as to other ontologies. This was achieved in several ways. We carried out an amalgamation of SAO terms with GO-CCO ones; as a result, nearly 100 new neuroscience-related terms were added to the GO. The GO-CCO also contains relationships to GO Biological Process and Molecular Function terms, as well as connecting to external ontologies such as the Cell Ontology (CL). Terms representing protein complexes in the Protein Ontology (PRO) reference GO-CCO terms for their species-generic counterparts. GO-CCO terms can also be used to search a variety of databases. Conclusions In this publication we provide an overview of the GO-CCO, its overall design, and some recent extensions that make use of additional spatial information. One of the most recent developments of the GO-CCO was the merging in of the SAO, resulting in a single unified Ontology designed to serve the needs of GO annotators as well as the specific needs of the neuroscience community.

Wasila M Dahdul - One of the best experts on this subject based on the ideXlab platform.

  • Enhanced XAO: the Ontology of Xenopus Anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase.
    Journal of biomedical semantics, 2013
    Co-Authors: Erik Segerdell, Wasila M Dahdul, Virgilio G. Ponferrada, Christina James-zorn, Kevin A. Burns, Joshua D. Fortriede, Peter D. Vize, Aaron M. Zorn
    Abstract:

    Background The African clawed frogs Xenopus laevis and Xenopus tropicalis are prominent animal model organisms. Xenopus research contributes to the understanding of genetic, developmental and molecular mechanisms underlying human disease. The Xenopus Anatomy Ontology (XAO) reflects the Anatomy and embryological development of Xenopus. The XAO provides consistent terminology that can be applied to anatomical feature descriptions along with a set of relationships that indicate how each anatomical entity is related to others in the embryo, tadpole, or adult frog. The XAO is integral to the functionality of Xenbase (http://www.xenbase.org), the Xenopus model organism database.

  • a unified Anatomy Ontology of the vertebrate skeletal system
    PLOS ONE, 2012
    Co-Authors: Wasila M Dahdul, James P Balhoff, Alexander D Diehl, Melissa Haendel, Hilmar Lapp, David C Blackburn, Brian K. Hall, John G Lundberg
    Abstract:

    The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleOntology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate Anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this Ontology will enable novel inquiries across the full spectrum of phenotypic diversity.

  • The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age
    Systematic biology, 2010
    Co-Authors: Wasila M Dahdul, Monte Westerfield, James P Balhoff, Hilmar Lapp, John G Lundberg, Peter E. Midford, Melissa A Haendel, Paula M Mabee
    Abstract:

    The rich knowledge of morphological variation among organisms reported in the systematic literature has remained in free-text format, impractical for use in large-scale synthetic phylogenetic work. This noncomputable format has also precluded linkage to the large knowledgebase of genomic, genetic, developmental, and phenotype data in model organism databases. We have undertaken an effort to prototype a curated, Ontology-based evolutionary morphology database that maps to these genetic databases (http://kb.phenoscape.org) to facilitate investigation into the mechanistic basis and evolution of phenotypic diversity. Among the first requirements in establishing this database was the development of a multispecies Anatomy Ontology with the goal of capturing anatomical data in a systematic and computable manner. An Ontology is a formal representation of a set of concepts with defined relationships between those concepts. Multispecies Anatomy ontologies in particular are an efficient way to represent the diversity of morphological structures in a clade of organisms, but they present challenges in their development relative to single-species Anatomy ontologies. Here, we describe the Teleost Anatomy Ontology (TAO), a multispecies Anatomy Ontology for teleost fishes derived from the Zebrafish Anatomical Ontology (ZFA) for the purpose of annotating varying morphological features across species. To facilitate interoperability with other Anatomy ontologies, TAO uses the Common Anatomy Reference Ontology as a template for its upper level nodes, and TAO and ZFA are synchronized, with zebrafish terms specified as subtypes of teleost terms. We found that the details of Ontology architecture have ramifications for querying, and we present general challenges in developing a multispecies Anatomy Ontology, including refinement of definitions, taxon-specific relationships among terms, and representation of taxonomically variable developmental pathways.

James P Balhoff - One of the best experts on this subject based on the ideXlab platform.

  • Matching arthropod Anatomy ontologies to the Hymenoptera Anatomy Ontology: results from a manual alignment
    Database : the journal of biological databases and curation, 2013
    Co-Authors: Matthew A. Bertone, James P Balhoff, István Mikó, Katja C. Seltmann, Matthew J. Yoder, Andrew R. Deans
    Abstract:

    Matching is an important step for increasing interoperability between heterogeneous ontologies. Here, we present alignments we produced as domain experts, using a manual mapping process, between the Hymenoptera Anatomy Ontology and other existing arthropod Anatomy ontologies (representing spiders, ticks, mosquitoes and Drosophila melanogaster). The resulting alignments contain from 43 to 368 mappings (correspondences), all derived from domain-expert input. Despite the many pairwise correspondences, only 11 correspondences were found in common between all ontologies, suggesting either major intrinsic differences between each Ontology or gaps in representing each group’s Anatomy. Furthermore, we compare our findings with putative correspondences from Bioportal (derived from LOOM software) and summarize the results in a total evidence alignment. We briefly discuss characteristics of the ontologies and issues with the matching process. Database URL: http://purl.obolibrary.org/obo/hao/2012-07-18/arthropod-mappings.obo

  • a unified Anatomy Ontology of the vertebrate skeletal system
    PLOS ONE, 2012
    Co-Authors: Wasila M Dahdul, James P Balhoff, Alexander D Diehl, Melissa Haendel, Hilmar Lapp, David C Blackburn, Brian K. Hall, John G Lundberg
    Abstract:

    The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleOntology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate Anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this Ontology will enable novel inquiries across the full spectrum of phenotypic diversity.

  • A revision of Evaniscus (Hymenoptera, Evaniidae) using Ontology-based semantic phenotype annotation.
    ZooKeys, 2012
    Co-Authors: Patricia L. Mullins, James P Balhoff, Ricardo Kawada, Andrew R. Deans
    Abstract:

    The Neotropical evaniid genus Evaniscus Szepligeti currently includes six species. Two new species are described, Evaniscus lansdownei Mullins, sp. n. from Colombia and Brazil and Evaniscus rafaeli Kawada, sp. n. from Brazil. Evaniscus sulcigenis Roman, syn. n., is synonymized under Evaniscus rufithorax Enderlein. An identification key to species of Evaniscus is provided. Thirty-five parsimony informative morphological characters are analyzed for six ingroup and four outgroup taxa. A topology resulting in a monophyletic Evaniscus is presented with Evaniscus tibialis and Evaniscus rafaeli as sister to the remaining Evaniscus species. The Hymenoptera Anatomy Ontology and other relevant biomedical ontologies are employed to create semantic phenotype statements in Entity-Quality (EQ) format for species descriptions. This approach is an early effort to formalize species descriptions and to make descriptive data available to other domains.

  • A hymenopterists' guide to the Hymenoptera Anatomy Ontology: Utility, clarification, and future directions
    Journal of Hymenoptera Research, 2012
    Co-Authors: Katja C. Seltmann, James P Balhoff, István Mikó, Matthew J. Yoder, Matthew A. Bertone, Mattias Forshage, Donat Agosti, Andrew D. Austin, Marek L. Borowiec, Seán G. Brady
    Abstract:

    Abstract Hymenoptera exhibit an incredible diversity of phenotypes, the result of ~240 million years of evolution and the primary subject of more than 250 years of research. Here we describe the history, development, and utility of the Hymenoptera Anatomy Ontology (HAO) and its associated applications. These resourc -es are designed to facilitate accessible and extensible research on hymenopteran phenotypes. Outreach with the hymenopterist community is of utmost importance to the HAO project, and this paper is a direct response to questions that arose from project workshops. In a concerted attempt to surmount barriers of understanding, especially regarding the format, utility, and development of the HAO, we discuss the roles of homology, “preferred terms”, and “structural equivalency”. We also outline the use of Universal Resource Identifiers (URIs) and posit that they are a key element necessary for increasing the objectivity and repeatability of science that references hymenopteran Anatomy. Pragmatically, we detail a mechanism (the “URI table”) by which authors can use URIs to link their published text to the HAO, and we describe an associated tool (the “Analyzer”) to derive these tables. These tools, and others, are available through the HAO Portal website (http://portal.hymao.org). We conclude by discussing the future of the HAO with respect to digital publication, cross-taxon Ontology alignment, the advent of semantic phenotypes, and community-based curation.

  • The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age
    Systematic biology, 2010
    Co-Authors: Wasila M Dahdul, Monte Westerfield, James P Balhoff, Hilmar Lapp, John G Lundberg, Peter E. Midford, Melissa A Haendel, Paula M Mabee
    Abstract:

    The rich knowledge of morphological variation among organisms reported in the systematic literature has remained in free-text format, impractical for use in large-scale synthetic phylogenetic work. This noncomputable format has also precluded linkage to the large knowledgebase of genomic, genetic, developmental, and phenotype data in model organism databases. We have undertaken an effort to prototype a curated, Ontology-based evolutionary morphology database that maps to these genetic databases (http://kb.phenoscape.org) to facilitate investigation into the mechanistic basis and evolution of phenotypic diversity. Among the first requirements in establishing this database was the development of a multispecies Anatomy Ontology with the goal of capturing anatomical data in a systematic and computable manner. An Ontology is a formal representation of a set of concepts with defined relationships between those concepts. Multispecies Anatomy ontologies in particular are an efficient way to represent the diversity of morphological structures in a clade of organisms, but they present challenges in their development relative to single-species Anatomy ontologies. Here, we describe the Teleost Anatomy Ontology (TAO), a multispecies Anatomy Ontology for teleost fishes derived from the Zebrafish Anatomical Ontology (ZFA) for the purpose of annotating varying morphological features across species. To facilitate interoperability with other Anatomy ontologies, TAO uses the Common Anatomy Reference Ontology as a template for its upper level nodes, and TAO and ZFA are synchronized, with zebrafish terms specified as subtypes of teleost terms. We found that the details of Ontology architecture have ramifications for querying, and we present general challenges in developing a multispecies Anatomy Ontology, including refinement of definitions, taxon-specific relationships among terms, and representation of taxonomically variable developmental pathways.