ArticleJournal of biomedical semantics2014
Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.
Article in Journal of biomedical semantics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Article
- Handedness in Animals and Plants.Biology · 2024Article
- Article
- Towards a clinically-based common coordinate framework for the human gut cell atlas: the gut models.BMC medical informatics and decision making · 2023Article
- Contribution of model organism phenotypes to the computational identification of human disease genes.Disease models & mechanisms · 2022Article
- Article
- Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms.Development (Cambridge, England) · 2021Article
- Mapping anatomical related entities to human body parts based on wikipedia in discharge summaries.BMC bioinformatics · 2019Article
- Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions.Biodiversity data journal · 2019Article
- COMICS: Cartoon Visualization of Omics Data in Spatial Context Using Anatomical Ontologies.Journal of proteome research · 2018Article
- Modifier Ontologies for frequency, certainty, degree, and coverage phenotype modifier.Biodiversity data journal · 2018Article
- Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems.Database : the journal of biological databases and curation · 2018Article
- The 'straight mouse': defining anatomical axes in 3D embryo models.Database : the journal of biological databases and curation · 2017Article
- Microbial phenomics information extractor (MicroPIE): a natural language processing tool for the automated acquisition of prokaryotic phenotypic characters from text sources.BMC bioinformatics · 2016Article
- PhenoImageShare: an image annotation and query infrastructure.Journal of biomedical semantics · 2016Article
- Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes.Molecular biology and evolution · 2016Article
- MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions.Journal of biomedical semantics · 2016Article
- Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals.PloS one · 2016Article
- ZFIN, The zebrafish model organism database: Updates and new directions.Genesis (New York, N.Y. : 2000) · 2015Article
- OTO: Ontology Term Organizer.BMC bioinformatics · 2015Article
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Authors and funding
7 authors.
Funding
Abstract
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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.