CARO – The Common Anatomy Reference Ontology

Haendel, Melissa; Neuhaus, Fabian; Osumi-Sutherland, David; Mabee, Paula M.; Mejino, Jos L.V.; Mungall, Chris; Smith, Barry

doi:10.1007/978-1-84628-885-2_16

Cited by 78 publications

(83 citation statements)

References 17 publications

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“…Although Ogloblin (1944) suggested that Waterston's structure might have glandular function, he never described any corresponding glands and applied the term "Waterston's organ" exclusively to the cuticle modifi cation. According to the Common Anatomy Reference Ontology (Haendel et al 2007) a simple organ is a multi-tissue structure. Because this cuticular modifi cation is not a multi-tissue structure we prefer to replace "organ" with "evaporatorium" from the heteropterists' lexicon.…”

Section: Methodsmentioning

confidence: 99%

Masner, a new genus of Ceraphronidae (Hymenoptera, Ceraphronoidea) described using controlled vocabularies

István¹,

Deans²

2009

829

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A ceraphronid wasp genus, Masner Mikó & Deans, gen. n., with one species, M. lubomirus Deans & Mikó, sp. n. is described from Australia and Fiji based on male specimens. Th is new genus challenges previous defi nitions of the two extant ceraphronoid families by sharing some character states with Megaspilidae (the presence of an expanded pterostigma and an occipital depression) and other character states with Ceraphronidae (the presence of uniramous anterior protibial spur, presence of a comb of the spur on the pro-and mesotibial spurs, a single mesotibial spur, an undivided synsternite, the presence of axillular setae, presence of Waterston's evaporatorium and the fusion of the parossiculus with the gonostipes). Masner is distinguishable from all other Ceraphronoidea by the sensillar patch present on fl agellomere 5 but absent from fl agellomeres 6-9 and the presence of a dorsally visible depression surrounding anterior part of the petiole. Th e limits of Ceraphronidae and Megaspilidae are reviewed, and we provide new characters for family level diagnosis and classifi cation. We also hypothesize that Masner is sister to the remaining Ceraphronidae.

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Section: Methodsmentioning

confidence: 99%

Masner, a new genus of Ceraphronidae (Hymenoptera, Ceraphronoidea) described using controlled vocabularies

István¹,

Deans²

2009

829

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“…Some ontologies represent structure, others represent function, yet others represent stages of development, and some draw on combinations of these, in ways that close off opportunities for automatic reasoning. The Foundry has created a roadmap for the incremental resolution of this problem through the initiation of the Common Anatomy Reference Ontology (CARO) 14 , which is providing guidelines both for modelorganism communities with legacy anatomy ontologies who wish to initiate reforms in the direction of compatibility and for communities who wish to build new ontologies from scratch. CARO is based on the toplevel types of the FMA and is serving as a template for the creation of the Fish Multi-Species, Ixodidae and Argasidae (tick), mosquito and Xenopus anatomy ontologies, and also as basis for reforms of the Drosophila and zebrafish anatomy ontologies 19 .…”

Section: Progress Thus Farmentioning

confidence: 99%

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration

et al. 2007

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The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or 'ontologies'. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium is pursuing a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing coordinated reform, and new ontologies are being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable and logically well formed and to incorporate accurate representations of biological reality. We describe this OBO Foundry initiative and provide guidelines for those who might wish to become involved.In the search for what is biologically and clinically significant in the swarms of data being generated by today's high-throughput technologies, a common strategy involves the creation and analysis of 'annotations' linking primary data to expressions in controlled, structured vocabularies, thereby making the data available to search and to algorithmic processing 1 . The most successful such endeavor, measured both by numbers of users and by reach across species and granularities, is the Gene Ontology (GO) 2 . There exist over 11 million annotations relating gene products described in the UniProt, Ensembl and other databases to terms in the GO3, of which half a million have been manually verified by specialist curators in different modelorganism communities on the basis of the analysis of experimental results reported in 52,000 scientific journal articles (http://www.ebi.ac.uk/GOA/). Data related to some 180,000 genes have been manually annotated in this way, an endeavor now being refined and systematized within the Reference Genome Project (US National Institutes of Health National Human Genome Research Institute grant 2P41HG002273-07), which will provide comprehensive GO annotations for both the human genome and a representative set of model-organism genomes in support of research on the primary molecular systems affecting human health. From retrospective mapping to prospective standardizationThe domain of molecular biology is marked by the availability of large amounts of well defined data that can be used without restriction as inputs to algorithmic processing. In the clinical domain, by contrast, only limited amounts of data are available for research purposes, and these still consist overwhelmingly of natural language text. Even where more systematic clinical data are available, the use of local coding schemes means that these data do not cumulate in ways useful to research 4 . One approach to solving this problem is the Unified Medical Language System (UMLS) 5 , a compendium of some 100 source vocabularies combined through a process of...

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“…BSPO classes for ‘anatomical compartment’ and ‘anatomical compartment boundary’ (11 classes) refer to anatomical structures defined by lineage restriction [6] rather than by axial position, and thus these classes will be moved to the Common Anatomy Reference Ontology (CARO) [7] in the future. Individual compartments and their boundaries are typically named with respect to some axis.…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2014

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BackgroundSpatial 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.ResultsBSPO 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’).ConclusionsThe 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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CARO – The Common Anatomy Reference Ontology

Cited by 78 publications

References 17 publications

Masner, a new genus of Ceraphronidae (Hymenoptera, Ceraphronoidea) described using controlled vocabularies

Masner, a new genus of Ceraphronidae (Hymenoptera, Ceraphronoidea) described using controlled vocabularies

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration

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

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