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Clarke JL, Cooper LD, Poelchau MF, Berardini TZ, Elser J, Farmer AD, Ficklin S, Kumari S, Laporte MA, Nelson RT, Sadohara R, Selby P, Thessen AE, Whitehead B, Sen TZ. Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium. Database (Oxford) 2023; 2023:baad076. [PMID: 37971715 PMCID: PMC10653126 DOI: 10.1093/database/baad076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/17/2023] [Indexed: 11/19/2023]
Abstract
Over the last couple of decades, there has been a rapid growth in the number and scope of agricultural genetics, genomics and breeding databases and resources. The AgBioData Consortium (https://www.agbiodata.org/) currently represents 44 databases and resources (https://www.agbiodata.org/databases) covering model or crop plant and animal GGB data, ontologies, pathways, genetic variation and breeding platforms (referred to as 'databases' throughout). One of the goals of the Consortium is to facilitate FAIR (Findable, Accessible, Interoperable, and Reusable) data management and the integration of datasets which requires data sharing, along with structured vocabularies and/or ontologies. Two AgBioData working groups, focused on Data Sharing and Ontologies, respectively, conducted a Consortium-wide survey to assess the current status and future needs of the members in those areas. A total of 33 researchers responded to the survey, representing 37 databases. Results suggest that data-sharing practices by AgBioData databases are in a fairly healthy state, but it is not clear whether this is true for all metadata and data types across all databases; and that, ontology use has not substantially changed since a similar survey was conducted in 2017. Based on our evaluation of the survey results, we recommend (i) providing training for database personnel in a specific data-sharing techniques, as well as in ontology use; (ii) further study on what metadata is shared, and how well it is shared among databases; (iii) promoting an understanding of data sharing and ontologies in the stakeholder community; (iv) improving data sharing and ontologies for specific phenotypic data types and formats; and (v) lowering specific barriers to data sharing and ontology use, by identifying sustainability solutions, and the identification, promotion, or development of data standards. Combined, these improvements are likely to help AgBioData databases increase development efforts towards improved ontology use, and data sharing via programmatic means. Database URL https://www.agbiodata.org/databases.
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Affiliation(s)
- Jennifer L Clarke
- Department of Statistics and Department of Food Science and Technology, University of Nebraska–Lincoln, 340 Hardin Hall North Wing, Lincoln, NE 68583, USA
| | - Laurel D Cooper
- Department of Botany and Plant Pathology, Oregon State University, 2503 Cordley Hall, Corvallis, OR 97331, USA
| | - Monica F Poelchau
- USDA, Agricultural Research Service, National Agricultural Library, 10301 Baltimore Ave, Beltsville 20705, USA
| | - Tanya Z Berardini
- The Arabidopsis Information Resource and Phoenix Bioinformatic, 39899 Balentine Drive, Suite 200, Newark, CA, USA
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, 2503 Cordley Hall, Corvallis, OR 97331, USA
| | - Andrew D Farmer
- National Center for Genome Resources, 2935 Rodeo Park Dr. E., Santa Fe, NM 87505, USA
| | - Stephen Ficklin
- Department of Horticulture, Washington State University, 249 Clark Hall, PO Box 646414, Pullman, WA 99164, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Marie-Angélique Laporte
- Digital Inclusion, Bioversity International, Parc Scientifique Agropolis II, 1990 Bd de la Lironde, Montpellier 34397, France
| | - Rex T Nelson
- USDA, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Iowa State University, 716 Farmhouse Lane, Ames, IA 50011, USA
| | - Rie Sadohara
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, 1066 Bogue St, East Lansing, MI 48824, USA
| | - Peter Selby
- School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, 215 Garden Avenue, Ithaca, NY 14850, USA
| | - Anne E Thessen
- Department of Biomedical Informatics, University of Colorado Anschutz, 1890 N. Revere Court, Mailstop F600, Aurora CO 80045, USA
| | - Brandon Whitehead
- Data Science and Informatics, Manaaki Whenua—Landcare Research, Ltd., Riddet Road, Massey University, Palmerston North 4472, New Zealand
| | - Taner Z Sen
- USDA, Agricultural Research Service, Crop Improvement Genetics Research Unit, Western Regional Research Center, 800 Buchanan St, Albany 94710, USA
- Department of Bioengineering, University of California, 306 Stanley Hall, Berkeley, CA 94720, USA
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2
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Vogt L, Mikó I, Bartolomaeus T. Anatomy and the type concept in biology show that ontologies must be adapted to the diagnostic needs of research. J Biomed Semantics 2022; 13:18. [PMID: 35761389 PMCID: PMC9235205 DOI: 10.1186/s13326-022-00268-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In times of exponential data growth in the life sciences, machine-supported approaches are becoming increasingly important and with them the need for FAIR (Findable, Accessible, Interoperable, Reusable) and eScience-compliant data and metadata standards. Ontologies, with their queryable knowledge resources, play an essential role in providing these standards. Unfortunately, biomedical ontologies only provide ontological definitions that answer What is it? questions, but no method-dependent empirical recognition criteria that answer How does it look? QUESTIONS Consequently, biomedical ontologies contain knowledge of the underlying ontological nature of structural kinds, but often lack sufficient diagnostic knowledge to unambiguously determine the reference of a term. RESULTS We argue that this is because ontology terms are usually textually defined and conceived as essentialistic classes, while recognition criteria often require perception-based definitions because perception-based contents more efficiently document and communicate spatial and temporal information-a picture is worth a thousand words. Therefore, diagnostic knowledge often must be conceived as cluster classes or fuzzy sets. Using several examples from anatomy, we point out the importance of diagnostic knowledge in anatomical research and discuss the role of cluster classes and fuzzy sets as concepts of grouping needed in anatomy ontologies in addition to essentialistic classes. In this context, we evaluate the role of the biological type concept and discuss its function as a general container concept for groupings not covered by the essentialistic class concept. CONCLUSIONS We conclude that many recognition criteria can be conceptualized as text-based cluster classes that use terms that are in turn based on perception-based fuzzy set concepts. Finally, we point out that only if biomedical ontologies model also relevant diagnostic knowledge in addition to ontological knowledge, they will fully realize their potential and contribute even more substantially to the establishment of FAIR and eScience-compliant data and metadata standards in the life sciences.
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Affiliation(s)
- Lars Vogt
- TIB Leibniz Information Centre for Science and Technology, Welfengarten 1B, 30167, Hannover, Germany.
| | - István Mikó
- Don Chandler Entomological Collection, University of New Hampshire, Durham, NH, USA
| | - Thomas Bartolomaeus
- Institut für Evolutionsbiologie und Ökologie, Universität Bonn, An der Immenburg 1, 53121, Bonn, Germany
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Porto DS, Dahdul WM, Lapp H, Balhoff JP, Vision TJ, Mabee PM, Uyeda J. Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge from Anatomy Ontologies. Syst Biol 2022; 71:1290-1306. [PMID: 35285502 PMCID: PMC9558846 DOI: 10.1093/sysbio/syac022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 02/09/2022] [Accepted: 03/05/2022] [Indexed: 11/18/2022] Open
Abstract
Morphology remains a primary source of phylogenetic information for many groups of organisms, and the only one for most fossil taxa. Organismal anatomy is not a collection of randomly assembled and independent “parts”, but instead a set of dependent and hierarchically nested entities resulting from ontogeny and phylogeny. How do we make sense of these dependent and at times redundant characters? One promising approach is using ontologies—structured controlled vocabularies that summarize knowledge about different properties of anatomical entities, including developmental and structural dependencies. Here, we assess whether evolutionary patterns can explain the proximity of ontology-annotated characters within an ontology. To do so, we measure phylogenetic information across characters and evaluate if it matches the hierarchical structure given by ontological knowledge—in much the same way as across-species diversity structure is given by phylogeny. We implement an approach to evaluate the Bayesian phylogenetic information (BPI) content and phylogenetic dissonance among ontology-annotated anatomical data subsets. We applied this to data sets representing two disparate animal groups: bees (Hexapoda: Hymenoptera: Apoidea, 209 chars) and characiform fishes (Actinopterygii: Ostariophysi: Characiformes, 463 chars). For bees, we find that BPI is not substantially explained by anatomy since dissonance is often high among morphologically related anatomical entities. For fishes, we find substantial information for two clusters of anatomical entities instantiating concepts from the jaws and branchial arch bones, but among-subset information decreases and dissonance increases substantially moving to higher-level subsets in the ontology. We further applied our approach to address particular evolutionary hypotheses with an example of morphological evolution in miniature fishes. While we show that phylogenetic information does match ontology structure for some anatomical entities, additional relationships and processes, such as convergence, likely play a substantial role in explaining BPI and dissonance, and merit future investigation. Our work demonstrates how complex morphological data sets can be interrogated with ontologies by allowing one to access how information is spread hierarchically across anatomical concepts, how congruent this information is, and what sorts of processes may play a role in explaining it: phylogeny, development, or convergence. [Apidae; Bayesian phylogenetic information; Ostariophysi; Phenoscape; phylogenetic dissonance; semantic similarity.]
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Affiliation(s)
- Diego S Porto
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, 926 West Campus Drive, Blacksburg, VA 24061, USA
| | - Wasila M Dahdul
- UCI Libraries,University of California, Irvine, Irvine, CA 92623, USA
- Department of Biology, University of South Dakota, 414 East Clark Street, Vermillion, SD 57069, USA
| | - Hilmar Lapp
- Center for Genomic and Computational Biology, Duke University, 101 Science Drive, Durham, NC 27708, USA
| | - James P Balhoff
- Renaissance Computing Institute, University of North Carolina, 100 Europa Drive, Suite 540, Chapel Hill, NC 27517, USA
| | - Todd J Vision
- Department of Biology and School of Information and Library Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Paula M Mabee
- Department of Biology, University of South Dakota, 414 East Clark Street, Vermillion, SD 57069, USA
- Battelle, National Ecological Observatory Network, Boulder, CO 80301, USA
| | - Josef Uyeda
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, 926 West Campus Drive, Blacksburg, VA 24061, USA
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Sidlauskas BL, Assega FM, Melo BF, Oliveira C, Birindelli JLO. Total evidence phylogenetic analysis reveals polyphyly of Anostomoides and uncovers an unexpectedly ancient genus of Anostomidae fishes (Characiformes). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The nearly 150 species of Anostomidae comprise one of the most diverse and taxonomically dynamic families of Neotropical freshwater fishes. A recent revision of the enigmatic and poorly diagnosed genus Anostomoides demonstrated that it contains two valid species, each with complicated taxonomic histories; however, that study did not address their phylogenetic placement. Herein, we integrate molecular and morphological data to demonstrate their distant evolutionary relationship, and thus the polyphyly of Anostomoides. While we reconstruct one of the species in a previously hypothesized placement within a clade also containing Laemolyta, Rhytiodus and Schizodon, the other represents a morphologically and genetically distinctive lineage that diverged early in the history of the family. We describe and illustrate the osteology of this remarkable species, discuss the evolutionary implications of its unique suite of features, and use those characteristics to diagnose a new genus that evolved independently of all other known members of the family for approximately 37 Myr.
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Affiliation(s)
- Brian L Sidlauskas
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
| | - Fernando M Assega
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Estadual de Londrina, Centro de Ciencias Biologicas, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, Campus Universitário, Londrina, PR, Brazil
| | - Bruno F Melo
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, R. Prof. Dr. Antonio C. W. Zanin, Rubião Jr, Botucatu, SP, Brazil
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, R. Prof. Dr. Antonio C. W. Zanin, Rubião Jr, Botucatu, SP, Brazil
| | - José L O Birindelli
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Estadual de Londrina, Centro de Ciencias Biologicas, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, Campus Universitário, Londrina, PR, Brazil
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5
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Enny A, Shanabag A, Thompson AW, Racicot B, Braasch I, Nakamura T. Cellular mechanisms of frontal bone development in spotted gar (Lepisosteus oculatus). Dev Dyn 2021; 250:1668-1682. [PMID: 33913218 DOI: 10.1002/dvdy.356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 04/17/2021] [Accepted: 04/19/2021] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND The cellular and molecular mechanisms initiating vertebrate cranial dermal bone formation is a conundrum in evolutionary and developmental biology. Decades of studies have determined the developmental processes of cranial dermal bones in various vertebrates and identified possible inducers of dermal bone. However, evolutionarily derived characters of current experimental model organisms, such as non-homologous frontal bones between teleosts and sarcopterygians, hinder investigations of ancestral and conserved mechanisms of vertebrate cranial dermal bone induction. Thus, investigating such mechanisms with animals diverging at evolutionarily informative phylogenetic nodes is imperative. RESULTS We investigated the cellular foundations of skull frontal bone formation in the spotted gar Lepisosteus oculatus, a basally branching non-teleost actinopterygian. Whole-mount bone and cartilage staining and hematoxylin-eosin section staining revealed that mesenchymal cell condensations in the frontal bone of spotted gar develop in close association with the underlying cartilage. We also identified novel aspects of frontal bone formation: enrichment of F-actin, cellular membranes, and E-cadherin in condensing cells, and extension of podia-like structures from osteoblasts to the frontal bone, which may be responsible for bone mineral transport. CONCLUSION This study highlights the process of frontal bone formation with dynamic architectural changes of mesenchymal cells in spotted gar, an emerging non-teleost fish model system, illuminating supposedly ancestral and likely conserved developmental mechanisms of skull bone formation among vertebrates.
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Affiliation(s)
- Alyssa Enny
- Department of Genetics, Rutgers the State University of New Jersey, Piscataway, New Jersey, USA
| | - Anusha Shanabag
- Department of Genetics, Rutgers the State University of New Jersey, Piscataway, New Jersey, USA
| | - Andrew W Thompson
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan, USA.,Program in Ecology, Evolution, and Behavior (EEB), Michigan State University, East Lansing, Michigan, USA
| | - Brett Racicot
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan, USA
| | - Ingo Braasch
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan, USA.,Program in Ecology, Evolution, and Behavior (EEB), Michigan State University, East Lansing, Michigan, USA
| | - Tetsuya Nakamura
- Department of Genetics, Rutgers the State University of New Jersey, Piscataway, New Jersey, USA
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6
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Sarmento-Soares LM, Martins-Pinheiro RF. A reappraisal of phylogenetic relationships among auchenipterid catfishes of the subfamily Centromochlinae and diagnosis of its genera (Teleostei: Siluriformes). PROCEEDINGS OF THE ACADEMY OF NATURAL SCIENCES OF PHILADELPHIA 2020. [DOI: 10.1635/053.167.0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Luisa Maria Sarmento-Soares
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Espírito Santo. Prédio Bárbara Weinberg, Campus de Goiabeiras, 29043-900, Vitória, ES, Brasil. http://orcid.org/0000-0002-8621-1794
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7
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Carvalho TP, Reis RE. A New Miniature Species of Acanthobunocephalus (Silurifomes: Aspredinidae) from the Lower Purus River Basin, Amazon Basin, Brazil. COPEIA 2020. [DOI: 10.1643/ci-19-309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Tiago P. Carvalho
- Laboratorio de Ictiología, Unidad de Ecología y Sistemática (UNESIS), Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7 No. 43-82, Bogotá D.C., Colombia; . Send reprint requests
| | - Roberto E. Reis
- Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Av. Ipiranga, 6681, 90619-900 Porto Alegre, RS, Brazil;
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8
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Mabee PM, Balhoff JP, Dahdul WM, Lapp H, Mungall CJ, Vision TJ. A Logical Model of Homology for Comparative Biology. Syst Biol 2020; 69:345-362. [PMID: 31596473 PMCID: PMC7672696 DOI: 10.1093/sysbio/syz067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 09/20/2019] [Accepted: 09/26/2019] [Indexed: 01/09/2023] Open
Abstract
There is a growing body of research on the evolution of anatomy in a wide variety of organisms. Discoveries in this field could be greatly accelerated by computational methods and resources that enable these findings to be compared across different studies and different organisms and linked with the genes responsible for anatomical modifications. Homology is a key concept in comparative anatomy; two important types are historical homology (the similarity of organisms due to common ancestry) and serial homology (the similarity of repeated structures within an organism). We explored how to most effectively represent historical and serial homology across anatomical structures to facilitate computational reasoning. We assembled a collection of homology assertions from the literature with a set of taxon phenotypes for the skeletal elements of vertebrate fins and limbs from the Phenoscape Knowledgebase. Using seven competency questions, we evaluated the reasoning ramifications of two logical models: the Reciprocal Existential Axioms (REA) homology model and the Ancestral Value Axioms (AVA) homology model. The AVA model returned all user-expected results in addition to the search term and any of its subclasses. The AVA model also returns any superclass of the query term in which a homology relationship has been asserted. The REA model returned the user-expected results for five out of seven queries. We identify some challenges of implementing complete homology queries due to limitations of OWL reasoning. This work lays the foundation for homology reasoning to be incorporated into other ontology-based tools, such as those that enable synthetic supermatrix construction and candidate gene discovery. [Homology; ontology; anatomy; morphology; evolution; knowledgebase; phenoscape.].
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Affiliation(s)
- Paula M Mabee
- Department of Biology, University of South Dakota, 414 East Clark Street, Vermillion, SD 57069, USA
| | - James P Balhoff
- Renaissance Computing Institute, University of North Carolina, 100 Europa Drive, Suite 540, Chapel Hill, NC 27517, USA
| | - Wasila M Dahdul
- Department of Biology, University of South Dakota, 414 East Clark Street, Vermillion, SD 57069, USA
| | - Hilmar Lapp
- Center for Genomic and Computational Biology, Duke University, 101 Science Drive, Durham, NC 27708, USA
| | - Christopher J Mungall
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Todd J Vision
- Department of Biology and School of Information and Library Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
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9
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Souza JDSE, Sarmento-Soares LM, Canto ALC, Ribeiro FRV. Description of a new species of Tatia from rio Tocantins drainage, central Brazil, with notes on Tatia simplex Mees, 1974 (Siluriformes, Auchenipteridae). NEOTROPICAL ICHTHYOLOGY 2020. [DOI: 10.1590/1982-0224-2019-0111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
ABSTRACT Tatia comprises twenty-five valid species, distributed in the main inland watersheds of South America, including the Orinoco, Essequibo, and coastal rivers of Suriname, Amazon, upper rio Paraná and São Francisco basins. A new species is described from tributaries of upper rio Manuel Alves on uplands of Serra Geral do Tocantins plateau, Tocantins State, Brazil. It is promptly distinguished from all congeners, except Tatia britskii, due to absence of an adipose fin. It differs from T. britskii by the longer caudal peduncle length (24.1–30.5% SL, mean 25.3 vs. 20.0–22.7, mean 20.9); caudal peduncle depth (10.9–16.8 SL, mean 14.1 vs. 9.4–10.5, mean 9.8), and anterior cranial border with mesethmoid width equals its length (vs. width approximately three times its length in T. britskii). Additionally, information regarding the poorly known species Tatia simplex originally described from rio das Mortes, is provided.
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Affiliation(s)
| | - Luisa M. Sarmento-Soares
- Universidade Federal do Espírito Santo, Brazil; Universidade Estadual de Feira de Santana, Brazil
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10
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The Spider Anatomy Ontology (SPD)—A Versatile Tool to Link Anatomy with Cross-Disciplinary Data. DIVERSITY 2019. [DOI: 10.3390/d11100202] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Spiders are a diverse group with a high eco-morphological diversity, which complicates anatomical descriptions especially with regard to its terminology. New terms are constantly proposed, and definitions and limits of anatomical concepts are regularly updated. Therefore, it is often challenging to find the correct terms, even for trained scientists, especially when the terminology has obstacles such as synonyms, disputed definitions, ambiguities, or homonyms. Here, we present the Spider Anatomy Ontology (SPD), which we developed combining the functionality of a glossary (a controlled defined vocabulary) with a network of formalized relations between terms that can be used to compute inferences. The SPD follows the guidelines of the Open Biomedical Ontologies and is available through the NCBO BioPortal (ver. 1.1). It constitutes of 757 valid terms and definitions, is rooted with the Common Anatomy Reference Ontology (CARO), and has cross references to other ontologies, especially of arthropods. The SPD offers a wealth of anatomical knowledge that can be used as a resource for any scientific study as, for example, to link images to phylogenetic datasets, compute structural complexity over phylogenies, and produce ancestral ontologies. By using a common reference in a standardized way, the SPD will help bridge diverse disciplines, such as genomics, taxonomy, systematics, evolution, ecology, and behavior.
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11
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Vogt L. Towards a semantic approach to numerical tree inference in phylogenetics. Cladistics 2018; 34:200-224. [PMID: 34645075 DOI: 10.1111/cla.12195] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2017] [Indexed: 12/24/2022] Open
Abstract
Conventional approaches to phylogeny reconstruction require a character analysis step prior to and methodologically separated from a numerical tree inference step. The former results in a character matrix that contains the empirical data analysed in the latter. This separation of steps involves various methodological and conceptual problems (e.g. homology assessment independent of tree inference and character optimization, character dependencies, discounting of alternative homology hypotheses). In morphology, the character analysis step covers the stages of morphological comparative studies, homology assessment and the identification and coding of morphological characters. Unfortunately, only the last stage requires some formalism, whereas the preceding stages are commonly regarded to be pre-rational and intuitive, which is why their reproducibility and analytical accessibility is limited. Here, I introduce a rational for a semantic approach to numerical tree inference that uses sets of semantic instance anatomies as data source instead of character matrices, thereby avoiding the above-mentioned problems. A semantic instance anatomy is an ontology-based description of the anatomical organization of a specimen in the form of a semantic graph. The semantic approach to numerical tree inference combines and integrates the steps of character analysis and numerical tree inference and makes both analytically accessible and communicable. Before outlining first steps for a research programme dedicated to the semantic approach to numerical tree inference, I discuss in detail the methodological, conceptual, and computational challenges and requirements that first have to be dealt with before adequate algorithms can be developed.
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Affiliation(s)
- Lars Vogt
- Institut für Evolutionsbiologie und Ökologie, Universität Bonn, An der Immenburg 1, Bonn, D-53121, Germany
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12
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Lundberg JG, Hendrickson DA, Luckenbill KR, Mariangeles AH. Satan's skeleton revealed: a tomographic and comparative osteology of Satan eurystomus, the subterranean Widemouth Blindcat (Siluriformes, Ictaluridae). PROCEEDINGS OF THE ACADEMY OF NATURAL SCIENCES OF PHILADELPHIA 2017. [DOI: 10.1635/053.165.0108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- John G. Lundberg
- Department of Ichthyology, The Academy of Natural Sciences, 1900 Benjamin Franklin Parkway, 19103-1195 Philadelphia, PA, USA
| | - Dean A. Hendrickson
- University of Texas Austin, Department of Integrative Biology, Biodiversity Collections (Texas Natural History Collections), 10100 Burnet Rd., PRC176 EAST/R4000, Austin, Texas 78758-4445 USA
| | - Kyle R. Luckenbill
- Department of Ichthyology, The Academy of Natural Sciences, 1900 Benjamin Franklin Parkway, 19103-1195 Philadelphia, PA, USA
| | - Arce H Mariangeles
- Department of Ichthyology, The Academy of Natural Sciences, 1900 Benjamin Franklin Parkway, 19103-1195 Philadelphia, PA, USA
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13
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Ali NM, Khan HA, Then AYH, Ving Ching C, Gaur M, Dhillon SK. Fish Ontology framework for taxonomy-based fish recognition. PeerJ 2017; 5:e3811. [PMID: 28929028 PMCID: PMC5602685 DOI: 10.7717/peerj.3811] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/25/2017] [Indexed: 11/20/2022] Open
Abstract
Life science ontologies play an important role in Semantic Web. Given the diversity in fish species and the associated wealth of information, it is imperative to develop an ontology capable of linking and integrating this information in an automated fashion. As such, we introduce the Fish Ontology (FO), an automated classification architecture of existing fish taxa which provides taxonomic information on unknown fish based on metadata restrictions. It is designed to support knowledge discovery, provide semantic annotation of fish and fisheries resources, data integration, and information retrieval. Automated classification for unknown specimens is a unique feature that currently does not appear to exist in other known ontologies. Examples of automated classification for major groups of fish are demonstrated, showing the inferred information by introducing several restrictions at the species or specimen level. The current version of FO has 1,830 classes, includes widely used fisheries terminology, and models major aspects of fish taxonomy, grouping, and character. With more than 30,000 known fish species globally, the FO will be an indispensable tool for fish scientists and other interested users.
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Affiliation(s)
- Najib M. Ali
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Haris A. Khan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Amy Y-Hui Then
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Chong Ving Ching
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Manas Gaur
- Wright State University, Kno.e.sis Center, Dayton, OH, United States of America
| | - Sarinder Kaur Dhillon
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
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14
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Vogt L. The logical basis for coding ontologically dependent characters. Cladistics 2017; 34:438-458. [DOI: 10.1111/cla.12209] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2017] [Indexed: 01/26/2023] Open
Affiliation(s)
- Lars Vogt
- Institut für Evolutionsbiologie und Ökologie; Universität Bonn; An der Immenburg 1 D-53121 Bonn Germany
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15
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Carvalho TP, Reis RE, Sabaj MH. Description of a New Blind and Rare Species ofXyliphius(Siluriformes: Aspredinidae) from the Amazon Basin Using High-Resolution Computed Tomography. COPEIA 2017. [DOI: 10.1643/ci-16-456] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Carvalho TP, Reis RE, Friel JP. A new species of Hoplomyzon (Siluriformes: Aspredinidae) from Maracaibo Basin, Venezuela: osteological description using high-resolution computed microtomography of a miniature species. NEOTROPICAL ICHTHYOLOGY 2017. [DOI: 10.1590/1982-0224-20160143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
ABSTRACT A new miniature species of banjo catfish of the genus Hoplomyzon is described from the Lake Maracaibo Basin in Venezuela. The new species is distinguished from all its congeners by the straight anterior margin of the mesethmoid (vs. a medial notch); a smooth and straight ventral surface of the premaxilla (vs. presence of bony knobs on the ventral surface of premaxilla); absence of teeth on dentary (vs. teeth present on dentary); configuration of ventral vertebral processes anterior to anal fin, which are composed of single processes anterior to anal-fin pterygiophore (vs. paired process); presence of several filamentous barbel-like structures on the ventral surface of head of adults (vs. small papillous structures in the ventral surface of head of adults); and 8 anal-fin rays (vs. 6 or 7). An extensive osteological description is made of the holotype using high-resolution x-ray computed microtomography (HRXCT).
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Affiliation(s)
- Tiago P. Carvalho
- Universidade Federal do Rio Grande do Sul, Brazil; Drexel University, USA
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17
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Carvalho TP, Lundberg JG, Baskin JN, Friel JP, Reis RE. A new species of the blind and miniature genusMicromyzonFriel and Lundberg, 1996 (Silurifomes: Aspredinidae) from the Orinoco River: describing catfish diversity using high-resolution computed tomography. PROCEEDINGS OF THE ACADEMY OF NATURAL SCIENCES OF PHILADELPHIA 2016. [DOI: 10.1635/053.165.0104] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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18
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Dececchi TA, Mabee PM, Blackburn DC. Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices. PLoS One 2016; 11:e0155680. [PMID: 27191170 PMCID: PMC4871461 DOI: 10.1371/journal.pone.0155680] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 05/03/2016] [Indexed: 01/17/2023] Open
Abstract
Databases of organismal traits that aggregate information from one or multiple sources can be leveraged for large-scale analyses in biology. Yet the differences among these data streams and how well they capture trait diversity have never been explored. We present the first analysis of the differences between phenotypes captured in free text of descriptive publications ('monographs') and those used in phylogenetic analyses ('matrices'). We focus our analysis on osteological phenotypes of the limbs of four extinct vertebrate taxa critical to our understanding of the fin-to-limb transition. We find that there is low overlap between the anatomical entities used in these two sources of phenotype data, indicating that phenotypes represented in matrices are not simply a subset of those found in monographic descriptions. Perhaps as expected, compared to characters found in matrices, phenotypes in monographs tend to emphasize descriptive and positional morphology, be somewhat more complex, and relate to fewer additional taxa. While based on a small set of focal taxa, these qualitative and quantitative data suggest that either source of phenotypes alone will result in incomplete knowledge of variation for a given taxon. As a broader community develops to use and expand databases characterizing organismal trait diversity, it is important to recognize the limitations of the data sources and develop strategies to more fully characterize variation both within species and across the tree of life.
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Affiliation(s)
- T. Alex Dececchi
- Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America
| | - Paula M. Mabee
- Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America
| | - David C. Blackburn
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
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19
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Druzinsky RE, Balhoff JP, Crompton AW, Done J, German RZ, Haendel MA, Herrel A, Herring SW, Lapp H, Mabee PM, Muller HM, Mungall CJ, Sternberg PW, Van Auken K, Vinyard CJ, Williams SH, Wall CE. Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. PLoS One 2016; 11:e0149102. [PMID: 26870952 PMCID: PMC4752357 DOI: 10.1371/journal.pone.0149102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 01/27/2016] [Indexed: 01/27/2023] Open
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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Affiliation(s)
- Robert E. Druzinsky
- Department of Oral Biology, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail:
| | - James P. Balhoff
- RTI International, Research Triangle Park, North Carolina, United States of America
| | - Alfred W. Crompton
- Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - James Done
- Division of Biology and Biological Engineering, M/C 156–29, California Institute of Technology, Pasadena, California, United States of America
| | - Rebecca Z. German
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, Ohio, United States of America
| | - Melissa A. Haendel
- Oregon Health and Science University, Portland, Oregon, United States of America
| | - Anthony Herrel
- Département d’Ecologie et de Gestion de la Biodiversité, Museum National d’Histoire Naturelle, Paris, France
| | - Susan W. Herring
- University of Washington, Department of Orthodontics, Seattle, Washington, United States of America
| | - Hilmar Lapp
- National Evolutionary Synthesis Center, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - Paula M. Mabee
- Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America
| | - Hans-Michael Muller
- Division of Biology and Biological Engineering, M/C 156–29, California Institute of Technology, Pasadena, California, United States of America
| | - Christopher J. Mungall
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Paul W. Sternberg
- Division of Biology and Biological Engineering, M/C 156–29, California Institute of Technology, Pasadena, California, United States of America
- Howard Hughes Medical Institute, M/C 156–29, California Institute of Technology, Pasadena, California, United States of America
| | - Kimberly Van Auken
- Division of Biology and Biological Engineering, M/C 156–29, California Institute of Technology, Pasadena, California, United States of America
| | - Christopher J. Vinyard
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, Ohio, United States of America
| | - Susan H. Williams
- Department of Biomedical Sciences, Ohio University Heritage College of Osteopathic Medicine, Athens, Ohio, United States of America
| | - Christine E. Wall
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
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20
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Göpel T, Richter S. The word is not enough: on morphemes, characters and ontological concepts. Cladistics 2016; 32:682-690. [DOI: 10.1111/cla.12145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2015] [Indexed: 11/28/2022] Open
Affiliation(s)
- Torben Göpel
- Allgemeine & Spezielle Zoologie; Institut für Biowissenschaften; Universität Rostock; Universitätsplatz 2 Rostock 18055 Germany
| | - Stefan Richter
- Allgemeine & Spezielle Zoologie; Institut für Biowissenschaften; Universität Rostock; Universitätsplatz 2 Rostock 18055 Germany
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21
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Sarmento-Soares LM, Lazzarotto H, Py-Daniel LR, Leitão RP. A new Centromochlus Kner, 1858 (Siluriformes: Auchenipteridae: Centromochlinae) from the transition between Amazon floodplain and Guiana shield, Brazil. NEOTROPICAL ICHTHYOLOGY 2016. [DOI: 10.1590/1982-0224-20160030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ABSTRACT Species of Centromochlus are widely distributed in South America, with records for major basins such as the Amazon and Orinoco, rivers draining the Guiana Shield such as the Essequibo, Courantyne (Corantijn), Coppename, Maroni, and Oyapock, and Brazilian Shield drainages as upper Paraná and São Francisco. In the last four years, three species of Centromochlus have been described, raising the total number of valid species to sixteen. The new species of Centromochlus described herein is diagnosed by having black ground color sharply delimited from a white underside by conspicuous wavy border. The new species is recorded from the Nhamundá, left bank tributary to the lower Amazon that drain from the Brazilian portion of the Guiana Shield. Although apparently similar to some Tatia species (e.g. Tatia musaica , T. carolae and T. melanoleuca ), the new species possess two conditions of the Weberian apparatus otherwise observed only in Centromochlus heckelii and C. existimatus among centromochlin catfishes. The new Centromochlus comprises small catfishes with adults ranging from 48 to 57 mm SL.
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22
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Lundberg JG, Luckenbill KR. The Extraordinary Occipito-Vertebral Skeleton and Swim Bladder of South AmericanHypophthalmusCatfishes (Siluriformes: Pimelodidae): Improved Illustration, Description, and Interpretation. COPEIA 2015. [DOI: 10.1643/cg-14-112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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Hilton EJ, Schnell NK, Konstantinidis P. When Tradition Meets Technology: Systematic Morphology of Fishes in the Early 21stCentury. COPEIA 2015. [DOI: 10.1643/ci-14-178] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Dececchi TA, Balhoff JP, Lapp H, Mabee PM. Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies. Syst Biol 2015; 64:936-52. [PMID: 26018570 PMCID: PMC4604830 DOI: 10.1093/sysbio/syv031] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 05/20/2015] [Indexed: 02/02/2023] Open
Abstract
The reality of larger and larger molecular databases and the need to integrate data scalably have presented a major challenge for the use of phenotypic data. Morphology is currently primarily described in discrete publications, entrenched in noncomputer readable text, and requires enormous investments of time and resources to integrate across large numbers of taxa and studies. Here we present a new methodology, using ontology-based reasoning systems working with the Phenoscape Knowledgebase (KB; kb.phenoscape.org), to automatically integrate large amounts of evolutionary character state descriptions into a synthetic character matrix of neomorphic (presence/absence) data. Using the KB, which includes more than 55 studies of sarcopterygian taxa, we generated a synthetic supermatrix of 639 variable characters scored for 1051 taxa, resulting in over 145,000 populated cells. Of these characters, over 76% were made variable through the addition of inferred presence/absence states derived by machine reasoning over the formal semantics of the source ontologies. Inferred data reduced the missing data in the variable character-subset from 98.5% to 78.2%. Machine reasoning also enables the isolation of conflicts in the data, that is, cells where both presence and absence are indicated; reports regarding conflicting data provenance can be generated automatically. Further, reasoning enables quantification and new visualizations of the data, here for example, allowing identification of character space that has been undersampled across the fin-to-limb transition. The approach and methods demonstrated here to compute synthetic presence/absence supermatrices are applicable to any taxonomic and phenotypic slice across the tree of life, providing the data are semantically annotated. Because such data can also be linked to model organism genetics through computational scoring of phenotypic similarity, they open a rich set of future research questions into phenotype-to-genome relationships.
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Affiliation(s)
| | - James P Balhoff
- National Evolutionary Synthesis Center, Durham, NC 27705, USA; University of North Carolina, Chapel Hill, NC 27599, USA
| | - Hilmar Lapp
- National Evolutionary Synthesis Center, Durham, NC 27705, USA; Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Paula M Mabee
- Department of Biology, University of South Dakota, Vermillion, SD 57069, USA;
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25
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Edmunds RC, Su B, Balhoff JP, Eames BF, Dahdul WM, Lapp H, Lundberg JG, Vision TJ, Dunham RA, Mabee PM, Westerfield M. Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes. Mol Biol Evol 2015; 33:13-24. [PMID: 26500251 PMCID: PMC4693980 DOI: 10.1093/molbev/msv223] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Phenotypes resulting from mutations in genetic model organisms can help reveal candidate genes for evolutionarily important phenotypic changes in related taxa. Although testing candidate gene hypotheses experimentally in nonmodel organisms is typically difficult, ontology-driven information systems can help generate testable hypotheses about developmental processes in experimentally tractable organisms. Here, we tested candidate gene hypotheses suggested by expert use of the Phenoscape Knowledgebase, specifically looking for genes that are candidates responsible for evolutionarily interesting phenotypes in the ostariophysan fishes that bear resemblance to mutant phenotypes in zebrafish. For this, we searched ZFIN for genetic perturbations that result in either loss of basihyal element or loss of scales phenotypes, because these are the ancestral phenotypes observed in catfishes (Siluriformes). We tested the identified candidate genes by examining their endogenous expression patterns in the channel catfish, Ictalurus punctatus. The experimental results were consistent with the hypotheses that these features evolved through disruption in developmental pathways at, or upstream of, brpf1 and eda/edar for the ancestral losses of basihyal element and scales, respectively. These results demonstrate that ontological annotations of the phenotypic effects of genetic alterations in model organisms, when aggregated within a knowledgebase, can be used effectively to generate testable, and useful, hypotheses about evolutionary changes in morphology.
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Affiliation(s)
| | - Baofeng Su
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University
| | | | - B Frank Eames
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Wasila M Dahdul
- National Evolutionary Synthesis Center, Durham, NC Department of Biology, University of South Dakota
| | - Hilmar Lapp
- National Evolutionary Synthesis Center, Durham, NC
| | - John G Lundberg
- Department of Ichthyology, The Academy of Natural Sciences, Philadelphia, Philadelphia, PA
| | - Todd J Vision
- National Evolutionary Synthesis Center, Durham, NC Department of Biology, University of North Carolina, Chapel Hill
| | - Rex A Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University
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26
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Birindelli JLO, Sarmento-Soares LM, Lima FCT. A new species of Centromochlus (Siluriformes, Auchenipteridae, Centromochlinae) from the middle Rio Tocantins basin, Brazil. JOURNAL OF FISH BIOLOGY 2015; 87:860-875. [PMID: 26287270 DOI: 10.1111/jfb.12750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 06/18/2015] [Indexed: 06/04/2023]
Abstract
A new species of the catfish genus Centromochlus (Auchenipteridae, Centromochlinae) is described. The new species is diagnosed by having numerous dark rounded blotches over the body and fins, dorsal-fin spine with serrations anteriorly and smooth posteriorly, anal fin of mature males with three unbranched and seven branched rays, anterior nuchal plate absent and posterior nuchal plate not extended ventrally. The new species is described from a small stream in the Estação Ecológica Serra Geral de Tocantins, a natural reserve in the centre of the Brazilian Cerrado, close to the watershed between the Rio Tocantins and the Rio São Francisco basins. The new species is possibly the sister taxon to the recently described Centromochlus meridionalis from the upper Rio Tapajós. Those two species share with Centromochlus perugiae, from the upper Amazon and upper Paraguay, derived features associated with the modified anal fin in sexually mature males.
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Affiliation(s)
- J L O Birindelli
- Departamento de Biologia Animal e Vegetal, Universidade Estadual de Londrina, Caixa Postal 10011, 86057-970, Londrina, PR, Brazil
| | - L M Sarmento-Soares
- Instituto Nacional da Mata Atlântica, Av. José Ruschi, 4, Centro, 29650-000, Santa Teresa, ES, Brazil
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Espírito Santo, Av. Marechal Campos, 1468, Prédio da Biologia, Campus de Maruípe, 29043-900, Vitória, ES, Brazil
| | - F C T Lima
- Museu de Zoologia da Universidade Estadual de Campinas "Adão José Cardoso", Caixa Postal 6109, 13083-863, Campinas, SP, Brazil
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27
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Manda P, Balhoff JP, Lapp H, Mabee P, Vision TJ. Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution. Genesis 2015. [PMID: 26220875 DOI: 10.1002/dvg.22878] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The abundance of phenotypic diversity among species can enrich our knowledge of development and genetics beyond the limits of variation that can be observed in model organisms. The Phenoscape Knowledgebase (KB) is designed to enable exploration and discovery of phenotypic variation among species. Because phenotypes in the KB are annotated using standard ontologies, evolutionary phenotypes can be compared with phenotypes from genetic perturbations in model organisms. To illustrate the power of this approach, we review the use of the KB to find taxa showing evolutionary variation similar to that of a query gene. Matches are made between the full set of phenotypes described for a gene and an evolutionary profile, the latter of which is defined as the set of phenotypes that are variable among the daughters of any node on the taxonomic tree. Phenoscape's semantic similarity interface allows the user to assess the statistical significance of each match and flags matches that may only result from differences in annotation coverage between genetic and evolutionary studies. Tools such as this will help meet the challenge of relating the growing volume of genetic knowledge in model organisms to the diversity of phenotypes in nature. The Phenoscape KB is available at http://kb.phenoscape.org.
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Affiliation(s)
- Prashanti Manda
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina.,US National Evolutionary Synthesis Center, Durham, North Carolina
| | - James P Balhoff
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina.,US National Evolutionary Synthesis Center, Durham, North Carolina
| | - Hilmar Lapp
- US National Evolutionary Synthesis Center, Durham, North Carolina.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina
| | - Paula Mabee
- Department of Biology, University of South Dakota, Vermillion, South Dakota
| | - Todd J Vision
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina.,US National Evolutionary Synthesis Center, Durham, North Carolina
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28
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Dahdul W, Dececchi TA, Ibrahim N, Lapp H, Mabee P. Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav040. [PMID: 25972520 PMCID: PMC4429748 DOI: 10.1093/database/bav040] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 04/05/2015] [Indexed: 11/28/2022]
Abstract
The diverse phenotypes of living organisms have been described for centuries, and though they may be digitized, they are not readily available in a computable form. Using over 100 morphological studies, the Phenoscape project has demonstrated that by annotating characters with community ontology terms, links between novel species anatomy and the genes that may underlie them can be made. But given the enormity of the legacy literature, how can this largely unexploited wealth of descriptive data be rendered amenable to large-scale computation? To identify the bottlenecks, we quantified the time involved in the major aspects of phenotype curation as we annotated characters from the vertebrate phylogenetic systematics literature. This involves attaching fully computable logical expressions consisting of ontology terms to the descriptions in character-by-taxon matrices. The workflow consists of: (i) data preparation, (ii) phenotype annotation, (iii) ontology development and (iv) curation team discussions and software development feedback. Our results showed that the completion of this work required two person-years by a team of two post-docs, a lead data curator, and students. Manual data preparation required close to 13% of the effort. This part in particular could be reduced substantially with better community data practices, such as depositing fully populated matrices in public repositories. Phenotype annotation required ∼40% of the effort. We are working to make this more efficient with Natural Language Processing tools. Ontology development (40%), however, remains a highly manual task requiring domain (anatomical) expertise and use of specialized software. The large overhead required for data preparation and ontology development contributed to a low annotation rate of approximately two characters per hour, compared with 14 characters per hour when activity was restricted to character annotation. Unlocking the potential of the vast stores of morphological descriptions requires better tools for efficiently processing natural language, and better community practices towards a born-digital morphology. Database URL:http://kb.phenoscape.org
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Affiliation(s)
- Wasila Dahdul
- Department of Biology, University of South Dakota, Vermillion, SD, USA, Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, USA and National Evolutionary Synthesis Center, Durham, NC, USA
| | - T Alexander Dececchi
- Department of Biology, University of South Dakota, Vermillion, SD, USA, Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, USA and National Evolutionary Synthesis Center, Durham, NC, USA
| | - Nizar Ibrahim
- Department of Biology, University of South Dakota, Vermillion, SD, USA, Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, USA and National Evolutionary Synthesis Center, Durham, NC, USA
| | - Hilmar Lapp
- Department of Biology, University of South Dakota, Vermillion, SD, USA, Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, USA and National Evolutionary Synthesis Center, Durham, NC, USA
| | - Paula Mabee
- Department of Biology, University of South Dakota, Vermillion, SD, USA, Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, USA and National Evolutionary Synthesis Center, Durham, NC, USA
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29
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Franz NM, Chen M, Yu S, Kianmajd P, Bowers S, Ludäscher B. Reasoning over taxonomic change: exploring alignments for the Perelleschus use case. PLoS One 2015; 10:e0118247. [PMID: 25700173 PMCID: PMC4336294 DOI: 10.1371/journal.pone.0118247] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 01/02/2015] [Indexed: 11/19/2022] Open
Abstract
Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations.
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Affiliation(s)
- Nico M. Franz
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Mingmin Chen
- Department of Computer Science, University of California Davis, Davis, California, United States of America
| | - Shizhuo Yu
- Department of Computer Science, University of California Davis, Davis, California, United States of America
| | - Parisa Kianmajd
- Department of Computer Science, University of California Davis, Davis, California, United States of America
| | - Shawn Bowers
- Department of Computer Science, Gonzaga University, Spokane, Washington, United States of America
| | - Bertram Ludäscher
- Department of Computer Science, University of California Davis, Davis, California, United States of America
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Dahdul WM, Cui H, Mabee PM, Mungall CJ, Osumi-Sutherland D, Walls RL, Haendel MA. Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. J Biomed Semantics 2014; 5:34. [PMID: 25140222 PMCID: PMC4137724 DOI: 10.1186/2041-1480-5-34] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 06/16/2014] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Spatial terminology is used in anatomy to indicate precise, relative positions of structures in an organism. While these terms are often standardized within specific fields of biology, they can differ dramatically across taxa. Such differences in usage can impair our ability to unambiguously refer to anatomical position when comparing anatomy or phenotypes across species. We developed the Biological Spatial Ontology (BSPO) to standardize the description of spatial and topological relationships across taxa to enable the discovery of comparable phenotypes. RESULTS BSPO currently contains 146 classes and 58 relations representing anatomical axes, gradients, regions, planes, sides, and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies. Spatial reasoning is further enhanced in anatomy ontologies by integrating spatial relations such as dorsal_to into class descriptions (e.g., 'dorsolateral placode' dorsal_to some 'epibranchial placode'). CONCLUSIONS The BSPO is currently used by projects that require standardized anatomical descriptors for phenotype annotation and ontology integration across a diversity of taxa. Anatomical location classes are also useful for describing phenotypic differences, such as morphological variation in position of structures resulting from evolution within and across species.
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Affiliation(s)
- Wasila M Dahdul
- Department of Biology, University of South Dakota, Vermillion, SD, USA
- National Evolutionary Synthesis Center, Durham, NC, USA
| | - Hong Cui
- School of Information Resource and Library Science, University of Arizona, Tucson, AZ, USA
| | - Paula M Mabee
- Department of Biology, University of South Dakota, Vermillion, SD, USA
| | | | | | - Ramona L Walls
- The iPlant Collaborative, Bio5 Institute, University of Arizona, Tucson, AZ, USA
| | - Melissa A Haendel
- Library and Department of Medical Informatics & Epidemiology, Oregon Health & Science University, Portland, OR, USA
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Haendel MA, Balhoff JP, Bastian FB, Blackburn DC, Blake JA, Bradford Y, Comte A, Dahdul WM, Dececchi TA, Druzinsky RE, Hayamizu TF, Ibrahim N, Lewis SE, Mabee PM, Niknejad A, Robinson-Rechavi M, Sereno PC, Mungall CJ. Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. J Biomed Semantics 2014; 5:21. [PMID: 25009735 PMCID: PMC4089931 DOI: 10.1186/2041-1480-5-21] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 03/25/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Elucidating disease and developmental dysfunction requires understanding variation in phenotype. Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. Multi-species anatomy ontologies (msAOs; vertebrate skeletal, vertebrate homologous, teleost, amphibian AOs) have been developed to represent 'natural' phenotypic variation across species. Our aim has been to integrate ssAOs and msAOs for various purposes, including establishing links between phenotypic variation and candidate genes. RESULTS Previously, msAOs contained a mixture of unique and overlapping content. This hampered integration and coordination due to the need to maintain cross-references or inter-ontology equivalence axioms to the ssAOs, or to perform large-scale obsolescence and modular import. Here we present the unification of anatomy ontologies into Uberon, a single ontology resource that enables interoperability among disparate data and research groups. As a consequence, independent development of TAO, VSAO, AAO, and vHOG has been discontinued. CONCLUSIONS The newly broadened Uberon ontology is a unified cross-taxon resource for metazoans (animals) that has been substantially expanded to include a broad diversity of vertebrate anatomical structures, permitting reasoning across anatomical variation in extinct and extant taxa. Uberon is a core resource that supports single- and cross-species queries for candidate genes using annotations for phenotypes from the systematics, biodiversity, medical, and model organism communities, while also providing entities for logical definitions in the Cell and Gene Ontologies. THE ONTOLOGY RELEASE FILES ASSOCIATED WITH THE ONTOLOGY MERGE DESCRIBED IN THIS MANUSCRIPT ARE AVAILABLE AT: http://purl.obolibrary.org/obo/uberon/releases/2013-02-21/ CURRENT ONTOLOGY RELEASE FILES ARE AVAILABLE ALWAYS AVAILABLE AT: http://purl.obolibrary.org/obo/uberon/releases/
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Affiliation(s)
- Melissa A Haendel
- Department of Medical Informatics & Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - James P Balhoff
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA ; National Evolutionary Synthesis Center, Durham, NC, USA
| | - Frederic B Bastian
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland ; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - David C Blackburn
- Department of Vertebrate Zoology and Anthropology, California Academy of Sciences, San Francisco, CA 94118, USA
| | | | - Yvonne Bradford
- The Zebrafish Model Organism Database, University of Oregon, Eugene, OR 97403, USA
| | - Aurelie Comte
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland ; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Wasila M Dahdul
- National Evolutionary Synthesis Center, Durham, NC, USA ; Department of Biology, University of South Dakota, Vermillion, SD 57069, USA
| | - Thomas A Dececchi
- Department of Biology, University of South Dakota, Vermillion, SD 57069, USA
| | - Robert E Druzinsky
- Department of Oral Biology, University of Illinois-Chicago, Chicago, IL 60612, USA
| | | | - Nizar Ibrahim
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA
| | - Suzanna E Lewis
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Paula M Mabee
- Department of Biology, University of South Dakota, Vermillion, SD 57069, USA
| | - Anne Niknejad
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland ; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland ; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Paul C Sereno
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA
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Ramírez MJ, Michalik P. Calculating structural complexity in phylogenies using ancestral ontologies. Cladistics 2014; 30:635-649. [DOI: 10.1111/cla.12075] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2014] [Indexed: 01/29/2023] Open
Affiliation(s)
- Martín J. Ramírez
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” - CONICET; Av. Angel Gallardo 470 C1405DJR Buenos Aires Argentina
| | - Peter Michalik
- Zoologisches Institut und Museum; Ernst-Moritz-Arndt-Universität; J.-S.-Bach-Str. 11/12 D-17489 Greifswald Germany
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Lundberg JG, Luckenbill KR, Babu KS, Ng HH. A tomographic osteology of the taxonomically puzzling catfishKryptoglanis shajii(Siluriformes, Siluroidei,incertae sedis): description and a first phylogenetic interpretation. PROCEEDINGS OF THE ACADEMY OF NATURAL SCIENCES OF PHILADELPHIA 2014. [DOI: 10.1635/053.163.0101] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Van Slyke CE, Bradford YM, Westerfield M, Haendel MA. The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio. J Biomed Semantics 2014; 5:12. [PMID: 24568621 PMCID: PMC3944782 DOI: 10.1186/2041-1480-5-12] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 02/07/2014] [Indexed: 01/07/2023] Open
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.
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Balhoff JP, Mikó I, Yoder MJ, Mullins PL, Deans AR. A semantic model for species description applied to the ensign wasps (hymenoptera: evaniidae) of New Caledonia. Syst Biol 2013; 62:639-59. [PMID: 23652347 PMCID: PMC3739881 DOI: 10.1093/sysbio/syt028] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 02/14/2013] [Accepted: 04/23/2013] [Indexed: 12/01/2022] Open
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.
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Affiliation(s)
- James P. Balhoff
- National Evolutionary Synthesis Center, Durham, NC 27705, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Insect Museum, Department of Entomology, North Carolina State University, Box 7613, Raleigh, NC 27695, USA; Department of Entomology, Pennsylvania State University, 501 ASI Building, University Park, PA 16802, USA; Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, MC 652 Champaign, IL 61820, USA; and Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - István Mikó
- National Evolutionary Synthesis Center, Durham, NC 27705, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Insect Museum, Department of Entomology, North Carolina State University, Box 7613, Raleigh, NC 27695, USA; Department of Entomology, Pennsylvania State University, 501 ASI Building, University Park, PA 16802, USA; Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, MC 652 Champaign, IL 61820, USA; and Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Matthew J. Yoder
- National Evolutionary Synthesis Center, Durham, NC 27705, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Insect Museum, Department of Entomology, North Carolina State University, Box 7613, Raleigh, NC 27695, USA; Department of Entomology, Pennsylvania State University, 501 ASI Building, University Park, PA 16802, USA; Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, MC 652 Champaign, IL 61820, USA; and Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Patricia L. Mullins
- National Evolutionary Synthesis Center, Durham, NC 27705, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Insect Museum, Department of Entomology, North Carolina State University, Box 7613, Raleigh, NC 27695, USA; Department of Entomology, Pennsylvania State University, 501 ASI Building, University Park, PA 16802, USA; Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, MC 652 Champaign, IL 61820, USA; and Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Andrew R. Deans
- National Evolutionary Synthesis Center, Durham, NC 27705, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Insect Museum, Department of Entomology, North Carolina State University, Box 7613, Raleigh, NC 27695, USA; Department of Entomology, Pennsylvania State University, 501 ASI Building, University Park, PA 16802, USA; Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, MC 652 Champaign, IL 61820, USA; and Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
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Park CA, Bello SM, Smith CL, Hu ZL, Munzenmaier DH, Nigam R, Smith JR, Shimoyama M, Eppig JT, Reecy JM. The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species. J Biomed Semantics 2013; 4:13. [PMID: 23937709 PMCID: PMC3851175 DOI: 10.1186/2041-1480-4-13] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 07/05/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The use of ontologies to standardize biological data and facilitate comparisons among datasets has steadily grown as the complexity and amount of available data have increased. Despite the numerous ontologies available, one area currently lacking a robust ontology is the description of vertebrate traits. A trait is defined as any measurable or observable characteristic pertaining to an organism or any of its substructures. While there are several ontologies to describe entities and processes in phenotypes, diseases, and clinical measurements, one has not been developed for vertebrate traits; the Vertebrate Trait Ontology (VT) was created to fill this void. DESCRIPTION Significant inconsistencies in trait nomenclature exist in the literature, and additional difficulties arise when trait data are compared across species. The VT is a unified trait vocabulary created to aid in the transfer of data within and between species and to facilitate investigation of the genetic basis of traits. Trait information provides a valuable link between the measurements that are used to assess the trait, the phenotypes related to the traits, and the diseases associated with one or more phenotypes. Because multiple clinical and morphological measurements are often used to assess a single trait, and a single measurement can be used to assess multiple physiological processes, providing investigators with standardized annotations for trait data will allow them to investigate connections among these data types. CONCLUSIONS The annotation of genomic data with ontology terms provides unique opportunities for data mining and analysis. Links between data in disparate databases can be identified and explored, a strategy that is particularly useful for cross-species comparisons or in situations involving inconsistent terminology. The VT provides a common basis for the description of traits in multiple vertebrate species. It is being used in the Rat Genome Database and Animal QTL Database for annotation of QTL data for rat, cattle, chicken, swine, sheep, and rainbow trout, and in the Mouse Phenome Database to annotate strain characterization data. In these databases, data are also cross-referenced to applicable terms from other ontologies, providing additional avenues for data mining and analysis. The ontology is available at http://bioportal.bioontology.org/ontologies/50138.
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Affiliation(s)
- Carissa A Park
- Department of Animal Science, Iowa State University, Ames, IA, USA.
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37
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Affiliation(s)
- Nico M. Franz
- School of Life Sciences; Arizona State University; PO Box 874501 Tempe AZ 85287-4501 USA
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Prykhozhij SV, Marsico A, Meijsing SH. Zebrafish Expression Ontology of Gene Sets (ZEOGS): a tool to analyze enrichment of zebrafish anatomical terms in large gene sets. Zebrafish 2013; 10:303-15. [PMID: 23656298 DOI: 10.1089/zeb.2012.0865] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The zebrafish (Danio rerio) is an established model organism for developmental and biomedical research. It is frequently used for high-throughput functional genomics experiments, such as genome-wide gene expression measurements, to systematically analyze molecular mechanisms. However, the use of whole embryos or larvae in such experiments leads to a loss of the spatial information. To address this problem, we have developed a tool called Zebrafish Expression Ontology of Gene Sets (ZEOGS) to assess the enrichment of anatomical terms in large gene sets. ZEOGS uses gene expression pattern data from several sources: first, in situ hybridization experiments from the Zebrafish Model Organism Database (ZFIN); second, it uses the Zebrafish Anatomical Ontology, a controlled vocabulary that describes connected anatomical structures; and third, the available connections between expression patterns and anatomical terms contained in ZFIN. Upon input of a gene set, ZEOGS determines which anatomical structures are overrepresented in the input gene set. ZEOGS allows one for the first time to look at groups of genes and to describe them in terms of shared anatomical structures. To establish ZEOGS, we first tested it on random gene selections and on two public microarray datasets with known tissue-specific gene expression changes. These tests showed that ZEOGS could reliably identify the tissues affected, whereas only very few enriched terms to none were found in the random gene sets. Next we applied ZEOGS to microarray datasets of 24 and 72 h postfertilization zebrafish embryos treated with beclomethasone, a potent glucocorticoid. This analysis resulted in the identification of several anatomical terms related to glucocorticoid-responsive tissues, some of which were stage-specific. Our studies highlight the ability of ZEOGS to extract spatial information from datasets derived from whole embryos, indicating that ZEOGS could be a useful tool to automatically analyze gene expression pattern features of any large zebrafish gene set.
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Betancur-R R, Broughton RE, Wiley EO, Carpenter K, López JA, Li C, Holcroft NI, Arcila D, Sanciangco M, Cureton Ii JC, Zhang F, Buser T, Campbell MA, Ballesteros JA, Roa-Varon A, Willis S, Borden WC, Rowley T, Reneau PC, Hough DJ, Lu G, Grande T, Arratia G, Ortí G. The tree of life and a new classification of bony fishes. PLOS CURRENTS 2013; 5:ecurrents.tol.53ba26640df0ccaee75bb165c8c26288. [PMID: 23653398 PMCID: PMC3644299 DOI: 10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288] [Citation(s) in RCA: 351] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The situation is most critical for a large clade of spiny-finned fishes, traditionally referred to as percomorphs, whose uncertain relationships have plagued ichthyologists for over a century. Most of what we know about the higher-level relationships among fish lineages has been based on morphology, but rapid influx of molecular studies is changing many established systematic concepts. We report a comprehensive molecular phylogeny for bony fishes that includes representatives of all major lineages. DNA sequence data for 21 molecular markers (one mitochondrial and 20 nuclear genes) were collected for 1410 bony fish taxa, plus four tetrapod species and two chondrichthyan outgroups (total 1416 terminals). Bony fish diversity is represented by 1093 genera, 369 families, and all traditionally recognized orders. The maximum likelihood tree provides unprecedented resolution and high bootstrap support for most backbone nodes, defining for the first time a global phylogeny of fishes. The general structure of the tree is in agreement with expectations from previous morphological and molecular studies, but significant new clades arise. Most interestingly, the high degree of uncertainty among percomorphs is now resolved into nine well-supported supraordinal groups. The order Perciformes, considered by many a polyphyletic taxonomic waste basket, is defined for the first time as a monophyletic group in the global phylogeny. A new classification that reflects our phylogenetic hypothesis is proposed to facilitate communication about the newly found structure of the tree of life of fishes. Finally, the molecular phylogeny is calibrated using 60 fossil constraints to produce a comprehensive time tree. The new time-calibrated phylogeny will provide the basis for and stimulate new comparative studies to better understand the evolution of the amazing diversity of fishes.
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Abstract
The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The situation is most critical for a large clade of spiny-finned fishes, traditionally referred to as percomorphs, whose uncertain relationships have plagued ichthyologists for over a century. Most of what we know about the higher-level relationships among fish lineages has been based on morphology, but rapid influx of molecular studies is changing many established systematic concepts. We report a comprehensive molecular phylogeny for bony fishes that includes representatives of all major lineages. DNA sequence data for 21 molecular markers (one mitochondrial and 20 nuclear genes) were collected for 1410 bony fish taxa, plus four tetrapod species and two chondrichthyan outgroups (total 1416 terminals). Bony fish diversity is represented by 1093 genera, 369 families, and all traditionally recognized orders. The maximum likelihood tree provides unprecedented resolution and high bootstrap support for most backbone nodes, defining for the first time a global phylogeny of fishes. The general structure of the tree is in agreement with expectations from previous morphological and molecular studies, but significant new clades arise. Most interestingly, the high degree of uncertainty among percomorphs is now resolved into nine well-supported supraordinal groups. The order Perciformes, considered by many a polyphyletic taxonomic waste basket, is defined for the first time as a monophyletic group in the global phylogeny. A new classification that reflects our phylogenetic hypothesis is proposed to facilitate communication about the newly found structure of the tree of life of fishes. Finally, the molecular phylogeny is calibrated using 60 fossil constraints to produce a comprehensive time tree. The new time-calibrated phylogeny will provide the basis for and stimulate new comparative studies to better understand the evolution of the amazing diversity of fishes.
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Vogt L, Nickel M, Jenner RA, Deans AR. The need for data standards in zoomorphology. J Morphol 2013; 274:793-808. [PMID: 23508988 DOI: 10.1002/jmor.20138] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Revised: 12/10/2012] [Accepted: 01/18/2013] [Indexed: 11/05/2022]
Abstract
eScience is a new approach to research that focuses on data mining and exploration rather than data generation or simulation. This new approach is arguably a driving force for scientific progress and requires data to be openly available, easily accessible via the Internet, and compatible with each other. eScience relies on modern standards for the reporting and documentation of data and metadata. Here, we suggest necessary components (i.e., content, concept, nomenclature, format) of such standards in the context of zoomorphology. We document the need for using data repositories to prevent data loss and how publication practice is currently changing, with the emergence of dynamic publications and the publication of digital datasets. Subsequently, we demonstrate that in zoomorphology the scientific record is still limited to published literature and that zoomorphological data are usually not accessible through data repositories. The underlying problem is that zoomorphology lacks the standards for data and metadata. As a consequence, zoomorphology cannot participate in eScience. We argue that the standardization of morphological data requires i) a standardized framework for terminologies for anatomy and ii) a formalized method of description that allows computer-parsable morphological data to be communicable, compatible, and comparable. The role of controlled vocabularies (e.g., ontologies) for developing respective terminologies and methods of description is discussed, especially in the context of data annotation and semantic enhancement of publications. Finally, we introduce the International Consortium for Zoomorphology Standards, a working group that is open to everyone and whose aim is to stimulate and synthesize dialog about standards. It is the Consortium's ultimate goal to assist the zoomorphology community in developing modern data and metadata standards, including anatomy ontologies, thereby facilitating the participation of zoomorphology in eScience.
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Affiliation(s)
- Lars Vogt
- Abteilung Zoologie und Evolutionsbiologie, Institut für Evolutionsbiologie und Ökologie, Fachgruppe Biologie, Universität Bonn; An der Immenburg 1, Bonn D-53121, Germany.
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Cooper L, Walls RL, Elser J, Gandolfo MA, Stevenson DW, Smith B, Preece J, Athreya B, Mungall CJ, Rensing S, Hiss M, Lang D, Reski R, Berardini TZ, Li D, Huala E, Schaeffer M, Menda N, Arnaud E, Shrestha R, Yamazaki Y, Jaiswal P. The plant ontology as a tool for comparative plant anatomy and genomic analyses. PLANT & CELL PHYSIOLOGY 2013; 54:e1. [PMID: 23220694 PMCID: PMC3583023 DOI: 10.1093/pcp/pcs163] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The Plant Ontology (PO; http://www.plantontology.org/) is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary ('ontology') of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded to include all green plants. The PO was the first multispecies anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. As of Release #18 (July 2012), there are about 2.2 million annotations linking PO terms to >110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and quantitative trait loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs.
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Affiliation(s)
- Laurel Cooper
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902, USA
- These authors contributed equally to this work
- These authors contributed equally to the development of the Plant Ontology
| | - Ramona L. Walls
- New York Botanical Garden, 2900 Southern Blvd., Bronx, NY 10458-5126, USA
- These authors contributed equally to this work
- These authors contributed equally to the development of the Plant Ontology
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902, USA
- These authors contributed equally to the development of the Plant Ontology
| | - Maria A. Gandolfo
- L.H. Bailey Hortorium, Department of Plant Biology, Cornell University, 412 Mann Library Building, Ithaca, NY 14853, USA
- These authors contributed equally to the development of the Plant Ontology
| | - Dennis W. Stevenson
- New York Botanical Garden, 2900 Southern Blvd., Bronx, NY 10458-5126, USA
- These authors contributed equally to the development of the Plant Ontology
| | - Barry Smith
- Department of Philosophy, University at Buffalo, 126 Park Hall, Buffalo, NY 14260, USA
- These authors contributed equally to the development of the Plant Ontology
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902, USA
| | - Balaji Athreya
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902, USA
| | - Christopher J. Mungall
- Berkeley Bioinformatics Open-Source Projects, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mailstop 64-121, Berkeley, CA 94720, USA
| | - Stefan Rensing
- Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Manuel Hiss
- Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Germany
- FRIAS - Freiburg Institute for Advanced Studies, University of Freiburg, Freiburg, Germany
| | - Tanya Z. Berardini
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Donghui Li
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Eva Huala
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Mary Schaeffer
- Agriculture Research Services, United States Department of Agriculture, Columbia, MO 65211, USA
- Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA
| | - Naama Menda
- Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY 148533, USA
| | - Elizabeth Arnaud
- Bioversity International, via dei Tre Denari, 174/a, Maccarese, Rome, Italy
| | - Rosemary Shrestha
- Genetic Resources Program, Centro Internacional de Mejoramiento de Maiz y Trigo (CIMMYT), Apdo. Postal 6-641, 06600 Mexico, D.F., Mexico
| | - Yukiko Yamazaki
- Center for Genetic Resource Information, National Institute of Genetics, Mishima, Shizuoka, 411-8540 Japan
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331-2902, USA
- These authors contributed equally to the development of the Plant Ontology
- *Corresponding author: E-mail,: ; Fax, +1-541-737-3573
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Dahdul WM, Balhoff JP, Blackburn DC, Diehl AD, Haendel MA, Hall BK, Lapp H, Lundberg JG, Mungall CJ, Ringwald M, Segerdell E, Van Slyke CE, Vickaryous MK, Westerfield M, Mabee PM. A unified anatomy ontology of the vertebrate skeletal system. PLoS One 2012; 7:e51070. [PMID: 23251424 PMCID: PMC3519498 DOI: 10.1371/journal.pone.0051070] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 10/30/2012] [Indexed: 11/19/2022] Open
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.
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Affiliation(s)
- Wasila M Dahdul
- Department of Biology, University of South Dakota, Vermillion, SD, USA.
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Vos RA, Balhoff JP, Caravas JA, Holder MT, Lapp H, Maddison WP, Midford PE, Priyam A, Sukumaran J, Xia X, Stoltzfus A. NeXML: rich, extensible, and verifiable representation of comparative data and metadata. Syst Biol 2012; 61:675-89. [PMID: 22357728 PMCID: PMC3376374 DOI: 10.1093/sysbio/sys025] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 07/29/2011] [Accepted: 02/07/2012] [Indexed: 12/13/2022] Open
Abstract
In scientific research, integration and synthesis require a common understanding of where data come from, how much they can be trusted, and what they may be used for. To make such an understanding computer-accessible requires standards for exchanging richly annotated data. The challenges of conveying reusable data are particularly acute in regard to evolutionary comparative analysis, which comprises an ever-expanding list of data types, methods, research aims, and subdisciplines. To facilitate interoperability in evolutionary comparative analysis, we present NeXML, an XML standard (inspired by the current standard, NEXUS) that supports exchange of richly annotated comparative data. NeXML defines syntax for operational taxonomic units, character-state matrices, and phylogenetic trees and networks. Documents can be validated unambiguously. Importantly, any data element can be annotated, to an arbitrary degree of richness, using a system that is both flexible and rigorous. We describe how the use of NeXML by the TreeBASE and Phenoscape projects satisfies user needs that cannot be satisfied with other available file formats. By relying on XML Schema Definition, the design of NeXML facilitates the development and deployment of software for processing, transforming, and querying documents. The adoption of NeXML for practical use is facilitated by the availability of (1) an online manual with code samples and a reference to all defined elements and attributes, (2) programming toolkits in most of the languages used commonly in evolutionary informatics, and (3) input-output support in several widely used software applications. An active, open, community-based development process enables future revision and expansion of NeXML.
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45
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Block AJ, Mabee PM. Development of the mandibular, hyoid arch and gill arch skeleton in the Chinese barb Puntius semifasciolatus: comparisons of ossification sequences among Cypriniformes. JOURNAL OF FISH BIOLOGY 2012; 81:54-80. [PMID: 22747804 DOI: 10.1111/j.1095-8649.2012.03307.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The morphogenesis and sequence of ossification and chondrification of skeletal elements of the jaws, and hyoid arch and gill arches of Puntius semifasciolatus are described. These data provide a baseline for further studies and enable comparisons with other described cypriniforms. Some general patterns of ossification in the hyoid arch and branchial arches in cypriniforms were notable. First, the overall development is from anterior to posterior, with the exception of the fifth ceratobranchial bone, which ossifies first. Second, where ossification of iterated elements is sequential, it tends to proceed from posterior to anterior, even when more posterior chondrifications are the smallest in the series. Ossification of the ceratobranchial, epibranchial and pharyngobranchial bones tends to proceed from ventral to dorsal. The comparisons revealed small sets of skeletal elements whose ossification sequence appears to be relatively conserved across cyprinid cypriniforms. Several potentially key timing changes in the ossification sequence of the jaws, hyoid arch and gill arches were identified, such as the accelerated timing of ossification of the fifth ceratobranchial bone, which may be unique to cypriniforms.
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Affiliation(s)
- A J Block
- Department of Biology, University of South Dakota, Vermillion, SD 57069, USA
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46
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Mabee BP, Balhoff JP, Dahdul WM, Lapp H, Midford PE, Vision TJ, Westerfield M. 500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton. ZEITSCHRIFT FUR ANGEWANDTE ICHTHYOLOGIE = JOURNAL OF APPLIED ICHTHYOLOGY 2012; 28:300-305. [PMID: 22736877 PMCID: PMC3377363 DOI: 10.1111/j.1439-0426.2012.01985.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 03/08/2012] [Indexed: 05/02/2023]
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.
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Affiliation(s)
- By Paula Mabee
- Department of Biology, 414 East Clark Street, University of South Dakota, Vermillion, South Dakota, United States of America
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47
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de Bono B, Grenon P, Sammut SJ. ApiNATOMY: A novel toolkit for visualizing multiscale anatomy schematics with phenotype-related information. Hum Mutat 2012; 33:837-48. [DOI: 10.1002/humu.22065] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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48
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Engeman JM, Mabee PM. Segmentation and fusion on the midline: basibranchial homologies in cypriniform fishes. J Morphol 2012; 273:725-36. [PMID: 22460806 DOI: 10.1002/jmor.20017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 12/17/2011] [Accepted: 02/05/2012] [Indexed: 11/09/2022]
Abstract
The development and homologies of the median elements of the ventral hyoid and branchial arches of Cypriniformes have been unclear. We compared the developmental morphology of this region across five species (Cycleptus elongatus, Luxilus zonatus, Danio rerio, Devario auropurpureus, and Cobitis striata), representing three of five major clades of cypriniforms. The development of basibranchial 1 is similar in catostomids and cyprinids, where a single, elongate, basihyal + anterior copula divides into separate elements. A gap develops between the posterior end of the basihyal cartilage and the anterior copula in catostomids but in cyprinids (Luxiluszonatus, Danio rerio, and Devarioauropurpureus) there is little separation and the basihyal and basibranchial 1 may grow close together or retain a cartilaginous connection (Danio rerio, several outgroups). In loaches and Gyrinocheilus, the gap posterior to the basihyal has been alternately interpreted as either the absence or posterior displacement of basibranchial 1. Uniquely among examined species, in Cobitis striata, the basihyal cartilage and anterior copula form as separate cartilages and remain distinct throughout development with a prominent gap between the basihyal and most anterior basibranchial, which we interpret as loss of basibranchial 1. In the posterior region associated with branchial arches 4 and 5, all examined species except Danio rerio, which has only a basibranchial 4 cartilage, have separate basibranchial 4 and 5 cartilages in early ontogeny. Basibranchials 4 and 5 remain separate in Cycleptus elongatus, Devario auropurpurea, and Cobitis striata, but fuse in Luxilus zonatus to form a posterior copula. The orientation of basibranchial 4 and 5 cartilages in Cobitis striata is similar to catostomids and cyprinids. The most posterior median element in the branchial arches, the post-ceratobranchial cartilage, generally forms as a separate cartilage in catostomids but in Cobitis striata is connected with basibranchial 5 cartilage from earliest appearance.
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Affiliation(s)
- Jeffrey M Engeman
- Department of Biology, University of South Dakota, Vermillion, SD 57069, USA
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49
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Deans AR, Yoder MJ, Balhoff JP. Time to change how we describe biodiversity. Trends Ecol Evol 2012; 27:78-84. [PMID: 22189359 DOI: 10.1016/j.tree.2011.11.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 11/18/2011] [Accepted: 11/22/2011] [Indexed: 01/18/2023]
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50
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Mungall CJ, Torniai C, Gkoutos GV, Lewis SE, Haendel MA. Uberon, an integrative multi-species anatomy ontology. Genome Biol 2012; 13:R5. [PMID: 22293552 PMCID: PMC3334586 DOI: 10.1186/gb-2012-13-1-r5] [Citation(s) in RCA: 409] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 01/31/2012] [Indexed: 01/20/2023] Open
Abstract
We present Uberon, an integrated cross-species ontology consisting of over 6,500 classes representing a variety of anatomical entities, organized according to traditional anatomical classification criteria. The ontology represents structures in a species-neutral way and includes extensive associations to existing species-centric anatomical ontologies, allowing integration of model organism and human data. Uberon provides a necessary bridge between anatomical structures in different taxa for cross-species inference. It uses novel methods for representing taxonomic variation, and has proved to be essential for translational phenotype analyses. Uberon is available at http://uberon.org
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Affiliation(s)
- Christopher J Mungall
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cycltotron Road MS 64-121, Berkeley, CA 94720, USA.
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