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A logical model of homology for comparative biology [article]

Paula M. Mabee, James P. Balhoff, Wasila M. Dahdul, Hilmar Lapp, Christopher J. Mungall, Todd J. Vision
2019 bioRxiv   pre-print
h o m o l o g y _ m e m b e r _ o f I n v e r s e O f : h a s _ h i s t o r i c a l _ h o m o l o g y _ m e m b e r h i s t o r i c a l _ h o m o l o g y _ m e m b e r _ o f !  ...  o l o g y _ m e m b e r _ o f v a l u e < p e c t o r a l _ f i n _ f o r e l i m b _ a n c e s t o r > ' f o r e l i m b ' S u b C l a s s O f h i s t o r i c a l _ h o m o l o g y _ m e m b e r _ o f  ... 
doi:10.1101/588822 fatcat:5jjxjbpozjg2vhriy4uttchgam

Hierarchy-guided Neural Networks for Species Classification [article]

Mohannad Elhamod, Kelly M. Diamond, A. Murat Maga, Yasin Bakis, Henry L. Bart, Paula Mabee, Wasila Dahdul, Jeremy Leipzig, Jane Greenberg, Brian Avants, Anuj Karpatne
2021 bioRxiv   pre-print
Lee, M. Sugiyama, U. Luxburg, I. Guyon, and R. Garnett, editors, Advances in Neural Information Processing Systems, volume 29, pages 4296-4304. Curran Associates, Inc., 2016.  ... 
doi:10.1101/2021.01.17.427006 fatcat:gywge4n62jbqjpm4jlc3seyjey

The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age

Wasila M. Dahdul, John G. Lundberg, Peter E. Midford, James P. Balhoff, Hilmar Lapp, Todd J. Vision, Melissa A. Haendel, Monte Westerfield, Paula M. Mabee
2010 Systematic Biology  
The rich knowledge of morphological variation among organisms reported in the systematic literature has remained in free-text format, impractical for use in large-scale synthetic phylogenetic work. This noncomputable format has also precluded linkage to the large knowledgebase of genomic, genetic, developmental, and phenotype data in model organism databases. We have undertaken an effort to prototype a curated, ontology-based evolutionary morphology database that maps to these genetic databases
more » ... (http://kb.phenoscape.org) to facilitate investigation into the mechanistic basis and evolution of phenotypic diversity. Among the first requirements in establishing this database was the development of a multispecies anatomy ontology with the goal of capturing anatomical data in a systematic and computable manner. An ontology is a formal representation of a set of concepts with defined relationships between those concepts. Multispecies anatomy ontologies in particular are an efficient way to represent the diversity of morphological structures in a clade of organisms, but they present challenges in their development relative to single-species anatomy ontologies. Here, we describe the Teleost Anatomy Ontology (TAO), a multispecies anatomy ontology for teleost fishes derived from the Zebrafish Anatomical Ontology (ZFA) for the purpose of annotating varying morphological features across species. To facilitate interoperability with other anatomy ontologies, TAO uses the Common Anatomy Reference Ontology as a template for its upper level nodes, and TAO and ZFA are synchronized, with zebrafish terms specified as subtypes of teleost terms. We found that the details of ontology architecture have ramifications for querying, and we present general challenges in developing a multispecies anatomy ontology, including refinement of definitions, taxon-specific relationships among terms, and representation of taxonomically variable developmental pathways.
doi:10.1093/sysbio/syq013 pmid:20547776 pmcid:PMC2885267 fatcat:v2kaej7yh5dafeitupyxd54yfy

Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge from Anatomy Ontologies

Diego S Porto, Wasila M Dahdul, Hilmar Lapp, James P Balhoff, Todd J Vision, Paula M Mabee, Josef Uyeda
2022 Systematic Biology  
et al. 2010a Dahdul et al. , 2012)) .  ...  Multispecies anatomy ontologies have been introduced for many taxa (e.g., amphibians: Maglia et al. 2007 ; fishes: Dahdul et al. 2010b; spiders: Ramírez and Michalik 2014; hymenopteran insects: Yoder  ... 
doi:10.1093/sysbio/syac022 pmid:35285502 fatcat:qgutbn2ugrcm7kxx5sk5pp7ymm

Phenex: Ontological Annotation of Phenotypic Diversity

James P. Balhoff, Wasila M. Dahdul, Cartik R. Kothari, Hilmar Lapp, John G. Lundberg, Paula Mabee, Peter E. Midford, Monte Westerfield, Todd J. Vision, Art F. Y. Poon
2010 PLoS ONE  
Phenex is a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic variation using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Despite the centrality of the phenotype to so much of biology, traditions for communicating information about phenotypes are idiosyncratic to different disciplines. Phenotypes seem to elude standardized descriptions due to
more » ... he variety of traits that compose them and the difficulty of capturing the complex forms and subtle differences among organisms that we can readily observe. Consequently, phenotypes are refractory to attempts at data integration that would allow computational analyses across studies and study systems. Phenex addresses this problem by allowing scientists to employ standard ontologies and syntax to link computable phenotype annotations to evolutionary character matrices, as well as to link taxa and specimens to ontological identifiers. Ontologies have become a foundational technology for establishing shared semantics, and, more generally, for capturing and computing with biological knowledge. Phenex can import character-by-taxon matrices in NEXUS format, but, importantly, it uses the new NeXML standard as its native file format. Phenex uses the extensible metadata facilities of NeXML, based on RDFa, to store 0ntological annotations within character-by-taxon matrix data using explicit semantic relationships. Phenex has been developed in the context of the Phenoscape project, where it has allowed data curators to transform a large body of morphologic character descriptions from the legacy systematics literature into computable phenotype annotations.
doi:10.1371/journal.pone.0010500 pmid:20463926 pmcid:PMC2864769 fatcat:psbpulgad5e3nl6wkylcwnwwpu

Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex

James P Balhoff, Wasila M Dahdul, T Dececchi, Hilmar Lapp, Paula M Mabee, Todd J Vision
2014 Journal of Biomedical Semantics  
Phenex (http://phenex.phenoscape.org/) is a desktop application for semantically annotating the phenotypic character matrix datasets common in evolutionary biology. Since its initial publication, we have added new features that address several major bottlenecks in the efficiency of the phenotype curation process: allowing curators during the data curation phase to provisionally request terms that are not yet available from a relevant ontology; supporting quality control against annotation
more » ... ines to reduce later manual review and revision; and enabling the sharing of files for collaboration among curators. Results: We decoupled data annotation from ontology development by creating an Ontology Request Broker (ORB) within Phenex. Curators can use the ORB to request a provisional term for use in data annotation; the provisional term can be automatically replaced with a permanent identifier once the term is added to an ontology. We added a set of annotation consistency checks to prevent common curation errors, reducing the need for later correction. We facilitated collaborative editing by improving the reliability of Phenex when used with online folder sharing services, via file change monitoring and continual autosave. Conclusions: With the addition of these new features, and in particular the Ontology Request Broker, Phenex users have been able to focus more effectively on data annotation. Phenoscape curators using Phenex have reported a smoother annotation workflow, with much reduced interruptions from ontology maintenance and file management issues.
doi:10.1186/2041-1480-5-45 pmid:25411634 pmcid:PMC4236444 fatcat:jm73jdhqxzbz7m73txajmnyrgy

Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes

Richard C. Edmunds, Baofeng Su, James P. Balhoff, B. Frank Eames, Wasila M. Dahdul, Hilmar Lapp, John G. Lundberg, Todd J. Vision, Rex A. Dunham, Paula M. Mabee, Monte Westerfield
2015 Molecular biology and evolution  
They also thank M. Sabaj for the image of his catfishes used in figure 1 and K. Luckenbill (Academy of Natural Sciences [ANSP], Philadelphia, PA) for his work in developing figure 2.  ...  Tris pH 9.5, 0.05 M MgCl 2 , 0.1 M NaCl, 0.1% Tween-20).  ...  Tris pH 9.5, 0.05 M MgCl 2 , 0.1 M NaCl, 0.1% Tween-20).  ... 
doi:10.1093/molbev/msv223 pmid:26500251 pmcid:PMC4693980 fatcat:5zlulwbgxzdnxg67lto7jjrhrm

Annotation of phenotypes using ontologies: a Gold Standard for the training and evaluation of natural language processing systems [article]

Wasila Dahdul, Prashanti Manda, Hong Cui, James P Balhoff, Alexander Dececchi, Nizar Ibrahim, Hilmar Lapp, Todd Vision, Paula M Mabee
2018 bioRxiv   pre-print
We thank M. Haendel and C. Mungall for suggestions on experiment design and ontology usage. We thank P. Chakrabarty, J. Clark, M. Coates, R. Hill, P. Skutschas, and J.  ...  The copyright holder for this preprint . http://dx.doi.org/10.1101/322156 doi: bioRxiv preprint first posted online May. 15, 2018; where p(N j ) = M ∈S(N j ) g(M ) q i=1 f (N i ) The I of two nodes is  ...  Dahdul, T. A. Dececchi and N. Ibrahim) and by Semantic CharaParser (SCP). The curators were randomly assigned identifiers C1, C2, and C3 at the beginning of the study.  ... 
doi:10.1101/322156 fatcat:xsnyvtqwlrgm5c7m24zyv2axee

Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature

Wasila M. Dahdul, James P. Balhoff, Jeffrey Engeman, Terry Grande, Eric J. Hilton, Cartik Kothari, Hilmar Lapp, John G. Lundberg, Peter E. Midford, Todd J. Vision, Monte Westerfield, Paula M. Mabee (+1 others)
2010 PLoS ONE  
Blake, M. Haendel, S. Lewis, C. Mungall, M. Ringwald, and N. Washington provided useful advice in the course of this work.  ...  Dahdul) . Curators were trained one-on-one by the lead curator at annotation workshops or remotely by conference calls.  ... 
doi:10.1371/journal.pone.0010708 pmid:20505755 pmcid:PMC2873956 fatcat:etngae7hpna4nkd4ilm6vqd3zu

Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology

Wasila M Dahdul, Hong Cui, Paula M Mabee, Christopher J Mungall, David Osumi-Sutherland, Ramona L Walls, Melissa A Haendel
2014 Journal of Biomedical Semantics  
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
more » ... cross taxa to enable the discovery of comparable phenotypes. 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'). 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.
doi:10.1186/2041-1480-5-34 pmid:25140222 pmcid:PMC4137724 fatcat:twgbwlryszbwhfnwohfqjl6vqa

A Unified Anatomy Ontology of the Vertebrate Skeletal System

Wasila M. Dahdul, James P. Balhoff, David C. Blackburn, Alexander D. Diehl, Melissa A. Haendel, Brian K. Hall, Hilmar Lapp, John G. Lundberg, Christopher J. Mungall, Martin Ringwald, Erik Segerdell, Ceri E. Van Slyke (+4 others)
2012 PLoS ONE  
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
more » ... ecies-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.
doi:10.1371/journal.pone.0051070 pmid:23251424 pmcid:PMC3519498 fatcat:bqn6ahk3v5dxdja63dsslhu3aq

The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes

Peter E Midford, Thomas Dececchi, James P Balhoff, Wasila M Dahdul, Nizar Ibrahim, Hilmar Lapp, John G Lundberg, Paula M Mabee, Paul C Sereno, Monte Westerfield, Todd J Vision, David C Blackburn
2013 Journal of Biomedical Semantics  
Conway for providing information on the taxonomy of Cypriniformes, M. Sabaj Pérez, M. Coburn, T. Grande, and E. Hilton for providing information on the taxonomy of other teleost groups, J.  ... 
doi:10.1186/2041-1480-4-34 pmid:24267744 pmcid:PMC4177199 fatcat:jeagurxhvzhvto23w4szndqa2y

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability

Alexander D. Diehl, Terrence F. Meehan, Yvonne M. Bradford, Matthew H. Brush, Wasila M. Dahdul, David S. Dougall, Yongqun He, David Osumi-Sutherland, Alan Ruttenberg, Sirarat Sarntivijai, Ceri E. Van Slyke, Nicole A. Vasilevsky (+3 others)
2016 Journal of Biomedical Semantics  
The Cell Ontology (CL) is an OBO Foundry candidate ontology covering the domain of canonical, natural biological cell types. Since its inception in 2005, the CL has undergone multiple rounds of revision and expansion, most notably in its representation of hematopoietic cells. For in vivo cells, the CL focuses on vertebrates but provides general classes that can be used for other metazoans, which can be subtyped in species-specific ontologies. Construction and content: Recent work on the CL has
more » ... ocused on extending the representation of various cell types, and developing new modules in the CL itself, and in related ontologies in coordination with the CL. For example, the Kidney and Urinary Pathway Ontology was used as a template to populate the CL with additional cell types. In addition, subtypes of the class 'cell in vitro' have received improved definitions and labels to provide for modularity with the representation of cells in the Cell Line Ontology and Reagent Ontology. Recent changes in the ontology development methodology for CL include a switch from OBO to OWL for the primary encoding of the ontology, and an increasing reliance on logical definitions for improved reasoning. Utility and discussion: The CL is now mandated as a metadata standard for large functional genomics and transcriptomics projects, and is used extensively for annotation, querying, and analyses of cell type specific data in sequencing consortia such as FANTOM5 and ENCODE, as well as for the NIAID ImmPort database and the Cell Image Library. The CL is also a vital component used in the modular construction of other biomedical ontologies-for example, the Gene Ontology and the cross-species anatomy ontology, Uberon, use CL to support the consistent representation of cell types across different levels of anatomical granularity, such as tissues and organs. Conclusions: The ongoing improvements to the CL make it a valuable resource to both the OBO Foundry community and the wider scientific community, and we continue to experience increased interest in the CL both among developers and within the user community.
doi:10.1186/s13326-016-0088-7 pmid:27377652 pmcid:PMC4932724 fatcat:otjugknudng4vilqqufaxppst4

Two new cis-Andean species of the South American catfish genus Megalonema allied to trans-Andean Megalonema xanthum, with description of a new subgenus (Siluriformes: Pimelodidae)

John G. Lundberg, Wasila M. Dahdul
2008 Neotropical Ichthyology  
Unambiguous synapomorphies indicate a sister-group relationship between M. amaxanthum and M. orixanthum, with M. xanthum basal to this pair.  ...  Eretmomegalonema new subgenus is established for M. xanthum, M. amaxanthum and M. orixanthum and supported by the uniquely synapomorphic paddle-like structure of its pelvic fin and hypertrophied basipterygium  ...  orixanthum 1 6 3 gill rakers on first branchial arch 18 19 20 / 25 26 27 28 29 M. xanthum 1 3 1 M. amaxanthum 1 1 2 M. orixanthum 1 3 total vertebrae 42 43 44 45 46 47 48 M. xanthum 1 1 18 3 M. amaxanthum  ... 
doi:10.1590/s1679-62252008000300018 fatcat:ykyhecmwsfcxra5ywypp3lkqfm

Emerging semantics to link phenotype and environment

Anne E. Thessen, Daniel E. Bunker, Pier Luigi Buttigieg, Laurel D. Cooper, Wasila M. Dahdul, Sami Domisch, Nico M. Franz, Pankaj Jaiswal, Carolyn J. Lawrence-Dill, Peter E. Midford, Christopher J. Mungall, Martín J. Ramírez (+10 others)
2015 PeerJ  
For example, several independent anatomy ontologies for vertebrates (teleost (Dahdul et al., 2010) ; amphibian (Maglia, Leopold & Pugener, 2007) ; vertebrate skeletal (Dahdul et al., 2012) , and vertebrate  ...  The time and effort spent on maintaining alignments and interoperability can be eliminated if shared community resources are instead developed (Dahdul et al., 2015) .  ...  Thessen analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper. • Wasila M.  ... 
doi:10.7717/peerj.1470 pmid:26713234 pmcid:PMC4690371 fatcat:6i47asuri5cabkiywg5stydqbe
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