124 results on '"Balhoff, James P"'
Search Results
102. A hymenopterists’ guide to the Hymenoptera Anatomy Ontology:utility, clarification, and future directions
- Author
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Seltmann, Katja C., Yoder, Matthew J., Miko, Istvan, Forshage, Mattias, Bertone, Matthew A., Deans, Andrew R., Agosti, Donat, Austin, Andrew D., Balhoff, James P., Borowiec, Marek L., Brady, Seán G., Broad, Gavin R., Brothers, Denis J., Burks, Roger A., Buffington, Matthew L., Campbell, Heather M., Dew, Kelly J., Ernst, Andrew F., Fernández-Triana, José L., Gates, Michael W., Gibson, Gary A. P., Jennings, John T., Johnson, Norman F., Karlsson, Dave, Kawada, Ricardo, Krogsmann, Lars, Kula, Robert R., Mullins, Patricia L., Ohl, Michael, Rasmussen, Claus, Ronquist, Fredrik, Schulmeister, Susanne, Sharkey, Michael J., Talamas, Elijah, Tucker, Erika, Vilhelmsen, Lars, Ward, Philip S., Wharton, Robert A., Seltmann, Katja C., Yoder, Matthew J., Miko, Istvan, Forshage, Mattias, Bertone, Matthew A., Deans, Andrew R., Agosti, Donat, Austin, Andrew D., Balhoff, James P., Borowiec, Marek L., Brady, Seán G., Broad, Gavin R., Brothers, Denis J., Burks, Roger A., Buffington, Matthew L., Campbell, Heather M., Dew, Kelly J., Ernst, Andrew F., Fernández-Triana, José L., Gates, Michael W., Gibson, Gary A. P., Jennings, John T., Johnson, Norman F., Karlsson, Dave, Kawada, Ricardo, Krogsmann, Lars, Kula, Robert R., Mullins, Patricia L., Ohl, Michael, Rasmussen, Claus, Ronquist, Fredrik, Schulmeister, Susanne, Sharkey, Michael J., Talamas, Elijah, Tucker, Erika, Vilhelmsen, Lars, Ward, Philip S., and Wharton, Robert A.
- Published
- 2012
103. A Unified Anatomy Ontology of the Vertebrate Skeletal System
- Author
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Dahdul, Wasila M., primary, Balhoff, James P., additional, Blackburn, David C., additional, Diehl, Alexander D., additional, Haendel, Melissa A., additional, Hall, Brian K., additional, Lapp, Hilmar, additional, Lundberg, John G., additional, Mungall, Christopher J., additional, Ringwald, Martin, additional, Segerdell, Erik, additional, Van Slyke, Ceri E., additional, Vickaryous, Matthew K., additional, Westerfield, Monte, additional, and Mabee, Paula M., additional
- Published
- 2012
- Full Text
- View/download PDF
104. Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature
- Author
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Dahdul, Wasila M., primary, Balhoff, James P., additional, Engeman, Jeffrey, additional, Grande, Terry, additional, Hilton, Eric J., additional, Kothari, Cartik, additional, Lapp, Hilmar, additional, Lundberg, John G., additional, Midford, Peter E., additional, Vision, Todd J., additional, Westerfield, Monte, additional, and Mabee, Paula M., additional
- Published
- 2010
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- View/download PDF
105. Phenex: Ontological Annotation of Phenotypic Diversity
- Author
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Balhoff, James P., primary, Dahdul, Wasila M., additional, Kothari, Cartik R., additional, Lapp, Hilmar, additional, Lundberg, John G., additional, Mabee, Paula, additional, Midford, Peter E., additional, Westerfield, Monte, additional, and Vision, Todd J., additional
- Published
- 2010
- Full Text
- View/download PDF
106. The 2006 NESCent Phyloinformatics Hackathon: A Field Report
- Author
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Lapp, Hilmar, primary, Bala, Sendu, additional, Balhoff, James P., additional, Bouck, Amy, additional, Goto, Naohisa, additional, Holder, Mark, additional, Holland, Richard, additional, Holloway, Alisha, additional, Katayama, Toshiaki, additional, Lewis, Paul O., additional, Mackey, Aaron J., additional, Osborne, Brian I., additional, Piel, William H., additional, Pond, Sergei L. Kosakovsky, additional, Poon, Art F.Y., additional, Qiu, Wei-Gang, additional, Stajich, Jason E., additional, Stoltzfus, Arlin, additional, Thierer, Tobias, additional, Vilella, Albert J., additional, Vos, Rutger A., additional, Zmasek, Christian M., additional, Zwickl, Derrick J., additional, and Vision, Todd J., additional
- Published
- 2007
- Full Text
- View/download PDF
107. Folding Wings like a Cockroach: A Review of Transverse Wing Folding Ensign Wasps (Hymenoptera: Evaniidae: Afrevania and Trissevania).
- Author
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Mikó, István, Copeland, Robert S., Balhoff, James P., Yoder, Matthew J., and Deans, Andrew R.
- Subjects
HYMENOPTERA ,COMPARATIVE anatomy ,COMPUTATIONAL biology ,ZOOLOGY ,ENTOMOLOGY ,NATURAL language processing - Abstract
We revise two relatively rare ensign wasp genera, whose species are restricted to Sub-Saharan Africa: Afrevania and Trissevania. Afrevania longipetiolata sp. nov., Trissevania heatherae sp. nov., T. hugoi sp. nov., T. mrimaensis sp. nov. and T. slideri sp. nov. are described, males and females of T. anemotis and Afrevania leroyi are redescribed, and an identification key for Trissevaniini is provided. We argue that Trissevania mrimaensis sp. nov. and T. heatherae sp. nov. populations are vulnerable, given their limited distributions and threats from mining activities in Kenya. We hypothesize that these taxa together comprise a monophyletic lineage, Trissevaniini, tr. nov., the members of which share the ability to fold their fore wings along two intersecting fold lines. Although wing folding of this type has been described for the hind wing of some insects four-plane wing folding of the fore wing has never been documented. The wing folding mechanism and the pattern of wing folds of Trissevaniini is shared only with some cockroach species (Blattodea). It is an interesting coincidence that all evaniids are predators of cockroach eggs. The major wing fold lines of Trissevaniini likely are not homologous to any known longitudinal anatomical structures on the wings of other Evaniidae. Members of the new tribe share the presence of a coupling mechanism between the fore wing and the mesosoma that is composed of a setal patch on the mesosoma and the retinaculum of the fore wing. While the setal patch is an evolutionary novelty, the retinaculum, which originally evolved to facilitate fore and hind wing coupling in Hymenoptera, exemplifies morphological exaptation. We also refine and clarify the Semantic Phenotype approach used in previous taxonomic revisions and explore the consequences of merging new with existing data. The way that semantic statements are formulated can evolve in parallel, alongside improvements to the ontologies themselves. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
108. Highly Specific and Quantitative Activation of STATs in 3T3-L1 Adipocytes
- Author
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Balhoff, James P., primary and Stephens, Jacqueline M., additional
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- 1998
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109. Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals
- Author
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Druzinsky, Robert E., Balhoff, James P., Crompton, Alfred W., Done, James, German, Rebecca Z., Haendel, Melissa A., Herrel, Anthony, Herring, Susan W., Lapp, Hilmar, Mabee, Paula M., Muller, Hans-Michael, Mungall, Christopher J., Sternberg, Paul W., Van Auken, Kimberly, Vinyard, Christopher J., Williams, Susan H., and Wall, Christine E.
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Database and Informatics Methods ,Database Searching ,Biology and Life Sciences ,Anatomy ,Comparative Anatomy ,Medicine and Health Sciences ,Zoology ,Computer and Information Sciences ,Data Management ,Ontologies ,Digestive System ,Mouth ,Mandible ,Animal Anatomy ,Physiology ,Physiological Processes ,Eating ,Organisms ,Animals ,Vertebrates ,Mammals ,Bone ,Biological Tissue ,Connective Tissue - Abstract
Background: In recent years large bibliographic databases have made much of the published literature of biology available for searches. However, the capabilities of the search engines integrated into these databases for text-based bibliographic searches are limited. To enable searches that deliver the results expected by comparative anatomists, an underlying logical structure known as an ontology is required. Development and Testing of the Ontology Here we present the Mammalian Feeding Muscle Ontology (MFMO), a multi-species ontology focused on anatomical structures that participate in feeding and other oral/pharyngeal behaviors. A unique feature of the MFMO is that a simple, computable, definition of each muscle, which includes its attachments and innervation, is true across mammals. This construction mirrors the logical foundation of comparative anatomy and permits searches using language familiar to biologists. Further, it provides a template for muscles that will be useful in extending any anatomy ontology. The MFMO is developed to support the Feeding Experiments End-User Database Project (FEED, https://feedexp.org/), a publicly-available, online repository for physiological data collected from in vivo studies of feeding (e.g., mastication, biting, swallowing) in mammals. Currently the MFMO is integrated into FEED and also into two literature-specific implementations of Textpresso, a text-mining system that facilitates powerful searches of a corpus of scientific publications. We evaluate the MFMO by asking questions that test the ability of the ontology to return appropriate answers (competency questions). We compare the results of queries of the MFMO to results from similar searches in PubMed and Google Scholar. Results and Significance Our tests demonstrate that the MFMO is competent to answer queries formed in the common language of comparative anatomy, but PubMed and Google Scholar are not. Overall, our results show that by incorporating anatomical ontologies into searches, an expanded and anatomically comprehensive set of results can be obtained. The broader scientific and publishing communities should consider taking up the challenge of semantically enabled search capabilities.
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- 2016
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110. Corrigenda: Mullins PL, Kawada R, Balhoff JP, Deans AR (2012) A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation. ZooKeys 223: 1-38, doi: 10.3897/zookeys.223.3572.
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Mullins, Patricia L., Kawada, Rico, Balhoff, James P., and Deans, Andrew R.
- Subjects
HYMENOPTERA ,ANIMAL species ,INSECTS - Abstract
A correction to the article "A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation" that was published in the previous issue is presented.
- Published
- 2013
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- View/download PDF
111. Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: results from a manual alignment.
- Author
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Bertone, Matthew A., Mikó, István, Yoder, Matthew J., Seltmann, Katja C., Balhoff, James P., and Deans, Andrew R.
- Subjects
ARTHROPOD diversity ,GENE mapping ,HYMENOPTERA ,FRESHWATER animals ,DROSOPHILA ,FRUIT flies - 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. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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112. A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation.
- Author
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Mullins, Patricia L., Kawada, Ricardo, Balhoff, James P., and Deans, Andrew R.
- Subjects
HYMENOPTERA ,PHENOTYPES ,BIOMEDICAL materials - Abstract
The Neotropical evaniid genus Evaniscus Szépligeti currently includes six species. Two new species are described, Evaniscus lansdownei Mullins, sp. n. from Colombia and Brazil and E. rafaeli Kawada, sp. n. from Brazil. Evaniscus sulcigenis Roman, syn. n., is synonymized under E. 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 E. tibialis and E. 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. [ABSTRACT FROM AUTHOR]
- Published
- 2012
- Full Text
- View/download PDF
113. A hymenopterists' guide to the Hymenoptera Anatomy Ontology: utility, clarification, and future directions.
- Author
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Seltmann, Katja C., Yoder, Matthew J., Mikó, István, Forshage, Mattias, Bertone, Matthew A., Agosti, Donat, Austin, Andrew D., Balhoff, James P., Borowiec, Marek L., Brady, Seán G., Broad, Gavin R., Brothers, Denis J., Burks, Roger A., Buffington, Matthew L., Campbell, Heather M., Dew, Kelly J., Ernst, Andrew F., Fernández-Triana, José L., Gates, Michael W., and Gibson, Gary A.P.
- Subjects
HYMENOPTERA ,INSECT anatomy ,PHENOTYPES ,CLASSIFICATION of insects ,MORPHOLOGY ,UNIFORM Resource Identifiers - 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 resources 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. [ABSTRACT FROM AUTHOR]
- Published
- 2012
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114. Evolutionary analysis of the well characterized endo 16 promoter reveals substantial variation within functional sites.
- Author
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Balhoff, James P. and Wray, Gregory A.
- Subjects
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NUCLEIC acids , *NUCLEOTIDES , *SEA urchins , *ECHINODERMATA , *BIOCHEMISTRY , *BIOLOGY - Abstract
The evolutionary mechanisms that operate on genetic variation within transcriptional regulatory sequences are not well under- stood. We present here an evolutionary analysis of an exceptionally well characterized cis-regulatory region, the endo 16 promoter of the purple sea urchin. Segregating variation reveals striking differences in the intensity of negative selection among regulatory modules, reflecting their distinct functional roles. Surprisingly, transcription-factor-binding sites are as polymorphic and as likely to contain fixed differences as flanking nucleotides. Whereas nucleotides in protein-binding sites in the most proximal regulatory module exhibit reduced variation, those in other modules tend to be more polymorphic than putatively nonfunctional nucleotides. Two unrelated large insertions at the same position within the promoter are segregating at low frequencies; one is a strong ectodermal repressor that contains 16 verified transcription-factor- binding sites. These results demonstrate that a simple relationship between conservation and function does not exist within this cis-regulatory region and highlight significant population heterogeneity in the fine structure of a well understood promoter. [ABSTRACT FROM AUTHOR]
- Published
- 2005
- Full Text
- View/download PDF
115. A Semantic Model for Species Description Applied to the Ensign Wasps (Hymenoptera: Evaniidae) of New Caledonia
- Author
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Balhoff, James P., Mullins, Patricia L., Deans, Andrew R., Mikó, István, and Yoder, Matthew J.
- Subjects
14. Life underwater - Abstract
Taxonomic descriptions are unparalleled sources of knowledge of life's phenotypic diversity. As natural language prose, these data sets are largely refractory to computation and integration with other sources of phenotypic data. By formalizing taxonomic descriptions using ontology-based semantic representation, we aim to increase the reusability and computability of taxonomists' primary data. Here, we present a revision of the ensign wasp (Hymenoptera: Evaniidae) fauna of New Caledonia using this new model for species description. Descriptive matrices, specimen data, and taxonomic nomenclature are gathered in a unified Web-based application, mx, then exported as both traditional taxonomic treatments and semantic statements using the OWL Web Ontology Language. Character:character-state combinations are then annotated following the entity–quality phenotype model, originally developed to represent mutant model organism phenotype data; concepts of anatomy are drawn from the Hymenoptera Anatomy Ontology and linked to phenotype descriptors from the Phenotypic Quality Ontology. The resulting set of semantic statements is provided in Resource Description Framework format. Applying the model to real data, that is, specimens, taxonomic names, diagnoses, descriptions, and redescriptions, provides us with a foundation to discuss limitations and potential benefits such as automated data integration and reasoner-driven queries. Four species of ensign wasp are now known to occur in New Caledonia: Szepligetella levipetiolata, Szepligetella deercreeki Deans and Mikó sp. nov., Szepligetella irwini Deans and Mikó sp. nov., and the nearly cosmopolitan Evania appendigaster. A fifth species, Szepligetella sericea, including Szepligetella impressa, syn. nov., has not yet been collected in New Caledonia but can be found on islands throughout the Pacific and so is included in the diagnostic key. [Biodiversity informatics; Evaniidae; New Caledonia; new species; ontology; semantic phenotypes; semantic species description; taxonomy.]
116. Folding Wings like a Cockroach: A Review of Transverse Wing Folding Ensign Wasps (Hymenoptera: Evaniidae: Afrevania and Trissevania).
- Author
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Mikó, István, Copeland, Robert S., Balhoff, James P., Yoder, Matthew J., and Deans, Andrew R.
- Subjects
- *
HYMENOPTERA , *COMPARATIVE anatomy , *COMPUTATIONAL biology , *ZOOLOGY , *ENTOMOLOGY , *NATURAL language processing - Abstract
We revise two relatively rare ensign wasp genera, whose species are restricted to Sub-Saharan Africa: Afrevania and Trissevania. Afrevania longipetiolata sp. nov., Trissevania heatherae sp. nov., T. hugoi sp. nov., T. mrimaensis sp. nov. and T. slideri sp. nov. are described, males and females of T. anemotis and Afrevania leroyi are redescribed, and an identification key for Trissevaniini is provided. We argue that Trissevania mrimaensis sp. nov. and T. heatherae sp. nov. populations are vulnerable, given their limited distributions and threats from mining activities in Kenya. We hypothesize that these taxa together comprise a monophyletic lineage, Trissevaniini, tr. nov., the members of which share the ability to fold their fore wings along two intersecting fold lines. Although wing folding of this type has been described for the hind wing of some insects four-plane wing folding of the fore wing has never been documented. The wing folding mechanism and the pattern of wing folds of Trissevaniini is shared only with some cockroach species (Blattodea). It is an interesting coincidence that all evaniids are predators of cockroach eggs. The major wing fold lines of Trissevaniini likely are not homologous to any known longitudinal anatomical structures on the wings of other Evaniidae. Members of the new tribe share the presence of a coupling mechanism between the fore wing and the mesosoma that is composed of a setal patch on the mesosoma and the retinaculum of the fore wing. While the setal patch is an evolutionary novelty, the retinaculum, which originally evolved to facilitate fore and hind wing coupling in Hymenoptera, exemplifies morphological exaptation. We also refine and clarify the Semantic Phenotype approach used in previous taxonomic revisions and explore the consequences of merging new with existing data. The way that semantic statements are formulated can evolve in parallel, alongside improvements to the ontologies themselves. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
117. Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies
- Author
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Nicolas Matentzoglu, Damien Goutte-Gattat, Shawn Zheng Kai Tan, James P Balhoff, Seth Carbon, Anita R Caron, William D Duncan, Joe E Flack, Melissa Haendel, Nomi L Harris, William R Hogan, Charles Tapley Hoyt, Rebecca C Jackson, HyeongSik Kim, Huseyin Kir, Martin Larralde, Julie A McMurry, James A Overton, Bjoern Peters, Clare Pilgrim, Ray Stefancsik, Sofia MC Robb, Sabrina Toro, Nicole A Vasilevsky, Ramona Walls, Christopher J Mungall, David Osumi-Sutherland, Goutte-Gattat, Damien [0000-0002-6095-8718], Tan, Shawn Zheng Kai [0000-0001-7258-9596], Balhoff, James P [0000-0002-8688-6599], Duncan, William D [0000-0001-9625-1899], Haendel, Melissa [0000-0001-9114-8737], Harris, Nomi L [0000-0001-6315-3707], Hogan, William R [0000-0002-9881-1017], Hoyt, Charles Tapley [0000-0003-4423-4370], Jackson, Rebecca C [0000-0003-4871-5569], Overton, James A [0000-0001-5139-5557], Peters, Bjoern [0000-0002-8457-6693], Pilgrim, Clare [0000-0002-1373-1705], Mungall, Christopher J [0000-0002-6601-2165], and Apollo - University of Cambridge Repository
- Subjects
FOS: Computer and information sciences ,Quality Control ,Metadata ,Biological Ontologies ,Databases, Factual ,Computer Science - Databases ,Databases (cs.DB) ,General Agricultural and Biological Sciences ,General Biochemistry, Genetics and Molecular Biology ,Software ,Information Systems ,Workflow - Abstract
Similar to managing software packages, managing the ontology life cycle involves multiple complex workflows such as preparing releases, continuous quality control checking, and dependency management. To manage these processes, a diverse set of tools is required, from command line utilities to powerful ontology engineering environments such as ROBOT. Particularly in the biomedical domain, which has developed a set of highly diverse yet inter-dependent ontologies, standardising release practices and metadata, and establishing shared quality standards, are crucial to enable interoperability. The Ontology Development Kit (ODK) provides a set of standardised, customisable, and automatically executable workflows, and packages all required tooling in a single Docker image. In this paper, we provide an overview of how the ODK works, show how it is used in practice, and describe how we envision it driving standardisation efforts in our community., 19 pages, 2 supplementary tables, 1 supplementary figure
- Published
- 2022
118. The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics.
- Author
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Matentzoglu N, Bello SM, Stefancsik R, Alghamdi SM, Anagnostopoulos AV, Balhoff JP, Balk MA, Bradford YM, Bridges Y, Callahan TJ, Caufield H, Cuzick A, Carmody LC, Caron AR, de Souza V, Engel SR, Fey P, Fisher M, Gehrke S, Grove C, Hansen P, Harris NL, Harris MA, Harris L, Ibrahim A, Jacobsen JOB, Köhler S, McMurry JA, Munoz-Fuentes V, Munoz-Torres MC, Parkinson H, Pendlington ZM, Pilgrim C, Robb SM, Robinson PN, Seager J, Segerdell E, Smedley D, Sollis E, Toro S, Vasilevsky N, Wood V, Haendel MA, Mungall CJ, McLaughlin JA, and Osumi-Sutherland D
- Abstract
Phenotypic data are critical for understanding biological mechanisms and consequences of genomic variation, and are pivotal for clinical use cases such as disease diagnostics and treatment development. For over a century, vast quantities of phenotype data have been collected in many different contexts covering a variety of organisms. The emerging field of phenomics focuses on integrating and interpreting these data to inform biological hypotheses. A major impediment in phenomics is the wide range of distinct and disconnected approaches to recording the observable characteristics of an organism. Phenotype data are collected and curated using free text, single terms or combinations of terms, using multiple vocabularies, terminologies, or ontologies. Integrating these heterogeneous and often siloed data enables the application of biological knowledge both within and across species. Existing integration efforts are typically limited to mappings between pairs of terminologies; a generic knowledge representation that captures the full range of cross-species phenomics data is much needed. We have developed the Unified Phenotype Ontology (uPheno) framework, a community effort to provide an integration layer over domain-specific phenotype ontologies, as a single, unified, logical representation. uPheno comprises (1) a system for consistent computational definition of phenotype terms using ontology design patterns, maintained as a community library; (2) a hierarchical vocabulary of species-neutral phenotype terms under which their species-specific counterparts are grouped; and (3) mapping tables between species-specific ontologies. This harmonized representation supports use cases such as cross-species integration of genotype-phenotype associations from different organisms and cross-species informed variant prioritization.
- Published
- 2024
- Full Text
- View/download PDF
119. The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences.
- Author
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Stefancsik R, Balhoff JP, Balk MA, Ball R, Bello SM, Caron AR, Chessler E, de Souza V, Gehrke S, Haendel M, Harris LW, Harris NL, Ibrahim A, Koehler S, Matentzoglu N, McMurry JA, Mungall CJ, Munoz-Torres MC, Putman T, Robinson P, Smedley D, Sollis E, Thessen AE, Vasilevsky N, Walton DO, and Osumi-Sutherland D
- Abstract
Existing phenotype ontologies were originally developed to represent phenotypes that manifest as a character state in relation to a wild-type or other reference. However, these do not include the phenotypic trait or attribute categories required for the annotation of genome-wide association studies (GWAS), Quantitative Trait Loci (QTL) mappings or any population-focused measurable trait data. Moreover, variations in gene expression in response to environmental disturbances even without any genetic alterations can also be associated with particular biological attributes. The integration of trait and biological attribute information with an ever increasing body of chemical, environmental and biological data greatly facilitates computational analyses and it is also highly relevant to biomedical and clinical applications. The Ontology of Biological Attributes (OBA) is a formalised, species-independent collection of interoperable phenotypic trait categories that is intended to fulfil a data integration role. OBA is a standardised representational framework for observable attributes that are characteristics of biological entities, organisms, or parts of organisms. OBA has a modular design which provides several benefits for users and data integrators, including an automated and meaningful classification of trait terms computed on the basis of logical inferences drawn from domain-specific ontologies for cells, anatomical and other relevant entities. The logical axioms in OBA also provide a previously missing bridge that can computationally link Mendelian phenotypes with GWAS and quantitative traits. The term components in OBA provide semantic links and enable knowledge and data integration across specialised research community boundaries, thereby breaking silos.
- Published
- 2023
- Full Text
- View/download PDF
120. Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems.
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Dahdul W, Manda P, Cui H, Balhoff JP, Dececchi TA, Ibrahim N, Lapp H, Vision T, and Mabee PM
- Subjects
- Humans, Data Curation methods, Data Mining methods, Gene Ontology, Natural Language Processing, Phenotype
- Abstract
Natural language descriptions of organismal phenotypes, a principal object of study in biology, are abundant in the biological literature. Expressing these phenotypes as logical statements using ontologies would enable large-scale analysis on phenotypic information from diverse systems. However, considerable human effort is required to make these phenotype descriptions amenable to machine reasoning. Natural language processing tools have been developed to facilitate this task, and the training and evaluation of these tools depend on the availability of high quality, manually annotated gold standard data sets. We describe the development of an expert-curated gold standard data set of annotated phenotypes for evolutionary biology. The gold standard was developed for the curation of complex comparative phenotypes for the Phenoscape project. It was created by consensus among three curators and consists of entity-quality expressions of varying complexity. We use the gold standard to evaluate annotations created by human curators and those generated by the Semantic CharaParser tool. Using four annotation accuracy metrics that can account for any level of relationship between terms from two phenotype annotations, we found that machine-human consistency, or similarity, was significantly lower than inter-curator (human-human) consistency. Surprisingly, allowing curatorsaccess to external information did not significantly increase the similarity of their annotations to the gold standard or have a significant effect on inter-curator consistency. We found that the similarity of machine annotations to the gold standard increased after new relevant ontology terms had been added. Evaluation by the original authors of the character descriptions indicated that the gold standard annotations came closer to representing their intended meaning than did either the curator or machine annotations. These findings point toward ways to better design software to augment human curators and the use of the gold standard corpus will allow training and assessment of new tools to improve phenotype annotation accuracy at scale.
- Published
- 2018
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- View/download PDF
121. INVESTIGATING THE IMPORTANCE OF ANATOMICAL HOMOLOGY FOR CROSS-SPECIES PHENOTYPE COMPARISONS USING SEMANTIC SIMILARITY. Accepted at Pacific Symposium on Biocomputing, 2016.
- Author
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Manda P, Mungall CJ, Balhoff JP, Lapp H, and Vision TJ
- Subjects
- Anatomy, Comparative statistics & numerical data, Animals, Computational Biology methods, Computational Biology statistics & numerical data, Evolution, Molecular, Humans, Mice, Phenotype, Semantics, Sequence Homology, Nucleic Acid, Species Specificity, Systems Integration, Zebrafish anatomy & histology, Zebrafish genetics, Anatomy, Comparative methods
- Abstract
There is growing use of ontologies for the measurement of cross-species phenotype similarity. Such similarity measurements contribute to diverse applications, such as identifying genetic models for human diseases, transferring knowledge among model organisms, and studying the genetic basis of evolutionary innovations. Two organismal features, whether genes, anatomical parts, or any other inherited feature, are considered to be homologous when they are evolutionarily derived from a single feature in a common ancestor. A classic example is the homology between the paired fins of fishes and vertebrate limbs. Anatomical ontologies that model the structural relations among parts may fail to include some known anatomical homologies unless they are deliberately added as separate axioms. The consequences of neglecting known homologies for applications that rely on such ontologies has not been well studied. Here, we examine how semantic similarity is affected when external homology knowledge is included. We measure phenotypic similarity between orthologous and non-orthologous gene pairs between humans and either mouse or zebrafish, and compare the inclusion of real with faux homology axioms. Semantic similarity was preferentially increased for orthologs when using real homology axioms, but only in the more divergent of the two species comparisons (human to zebrafish, not human to mouse), and the relative increase was less than 1% to non-orthologs. By contrast, inclusion of both real and faux random homology axioms preferentially increased similarities between genes that were initially more dissimilar in the other comparisons. Biologically meaningful increases in semantic similarity were seen for a select subset of gene pairs. Overall, the effect of including homology axioms on cross-species semantic similarity was modest at the levels of divergence examined here, but our results hint that it may be greater for more distant species comparisons.
- Published
- 2016
122. An overview of the BioCreative 2012 Workshop Track III: interactive text mining task.
- Author
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Arighi CN, Carterette B, Cohen KB, Krallinger M, Wilbur WJ, Fey P, Dodson R, Cooper L, Van Slyke CE, Dahdul W, Mabee P, Li D, Harris B, Gillespie M, Jimenez S, Roberts P, Matthews L, Becker K, Drabkin H, Bello S, Licata L, Chatr-aryamontri A, Schaeffer ML, Park J, Haendel M, Van Auken K, Li Y, Chan J, Muller HM, Cui H, Balhoff JP, Chi-Yang Wu J, Lu Z, Wei CH, Tudor CO, Raja K, Subramani S, Natarajan J, Cejuela JM, Dubey P, and Wu C
- Subjects
- Databases as Topic, Documentation, Humans, Software, Time Factors, Data Mining, Education
- Abstract
In many databases, biocuration primarily involves literature curation, which usually involves retrieving relevant articles, extracting information that will translate into annotations and identifying new incoming literature. As the volume of biological literature increases, the use of text mining to assist in biocuration becomes increasingly relevant. A number of groups have developed tools for text mining from a computer science/linguistics perspective, and there are many initiatives to curate some aspect of biology from the literature. Some biocuration efforts already make use of a text mining tool, but there have not been many broad-based systematic efforts to study which aspects of a text mining tool contribute to its usefulness for a curation task. Here, we report on an effort to bring together text mining tool developers and database biocurators to test the utility and usability of tools. Six text mining systems presenting diverse biocuration tasks participated in a formal evaluation, and appropriate biocurators were recruited for testing. The performance results from this evaluation indicate that some of the systems were able to improve efficiency of curation by speeding up the curation task significantly (∼1.7- to 2.5-fold) over manual curation. In addition, some of the systems were able to improve annotation accuracy when compared with the performance on the manually curated set. In terms of inter-annotator agreement, the factors that contributed to significant differences for some of the systems included the expertise of the biocurator on the given curation task, the inherent difficulty of the curation and attention to annotation guidelines. After the task, annotators were asked to complete a survey to help identify strengths and weaknesses of the various systems. The analysis of this survey highlights how important task completion is to the biocurators' overall experience of a system, regardless of the system's high score on design, learnability and usability. In addition, strategies to refine the annotation guidelines and systems documentation, to adapt the tools to the needs and query types the end user might have and to evaluate performance in terms of efficiency, user interface, result export and traditional evaluation metrics have been analyzed during this task. This analysis will help to plan for a more intense study in BioCreative IV.
- Published
- 2013
- Full Text
- View/download PDF
123. Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: results from a manual alignment.
- Author
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Bertone MA, Mikó I, Yoder MJ, Seltmann KC, Balhoff JP, and Deans AR
- Subjects
- Algorithms, Animals, Data Mining, Hymenoptera anatomy & histology
- 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.
- Published
- 2013
- Full Text
- View/download PDF
124. 500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton.
- Author
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Mabee BP, Balhoff JP, Dahdul WM, Lapp H, Midford PE, Vision TJ, and Westerfield M
- Abstract
The rich phenotypic diversity that characterizes the vertebrate skeleton results from evolutionary changes in regulation of genes that drive development. Although relatively little is known about the genes that underlie the skeletal variation among fish species, significant knowledge of genetics and development is available for zebrafish. Because developmental processes are highly conserved, this knowledge can be leveraged for understanding the evolution of skeletal diversity. We developed the Phenoscape Knowledgebase (KB; http://kb.phenoscape.org) to yield testable hypotheses of candidate genes involved in skeletal evolution. We developed a community anatomy ontology for fishes and ontology-based methods to represent complex free-text character descriptions of species in a computable format. With these tools, we populated the KB with comparative morphological data from the literature on over 2,500 teleost fishes (mainly Ostariophysi) resulting in over 500,000 taxon phenotype annotations. The KB integrates these data with similarly structured phenotype data from zebrafish genes (http://zfin.org). Using ontology-based reasoning, candidate genes can be inferred for the phenotypes that vary across taxa, thereby uniting genetic and phenotypic data to formulate evo-devo hypotheses. The morphological data in the KB can be browsed, sorted, and aggregated in ways that provide unprecedented possibilities for data mining and discovery.
- Published
- 2012
- Full Text
- View/download PDF
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