Foundational Model of Anatomy | NCBO BioPortal

Foundational Model of Anatomy Summary

Metrics

Number of classes:	83281
Number of individuals:	7
Number of properties:	186
Maximum depth:	21
Maximum number of siblings:	219
Average number of siblings:	54
Classes with a single subclass:	73 Classes with a single subclass 'Articular cartilage of superior articular process of vertebra' 'Brodmann area 20 of segment of parahippocampal gyrus' 'Costal element of sacral vertebra' 'Cytoplasmic inclusion' 'Deep lymphatic vessel of head' 'Dense-core granulated cell' 'Distal part of diaphysis' 'Epithelioid cell' 'Fetal artery' 'Ganglion of neuraxis' 'Gray matter of hypothalamus' 'Inner kinetochore of condensed chromosome' 'Intraorgan venous tree' 'Lamina of sacral vertebra' 'Lumen of trunk of median sacral artery' 'Lymphatic capillary' 'Membranous layer of superficial fascia' 'Middle muscle layer of organ' 'Naso-pharyngeal lymphoid tissue' 'Organ component of kidney' 'Outer kinetochore of condensed chromosome' 'Pars distalis of adenohypophysis' 'Pedicle of sacral segment' 'Physical attribute relationship' 'Posterolateral part of body of sacral segment' 'Primary lysosome' 'Proximal part of diaphysis' 'Pyramidal cell of cerebral cortex' 'Ribonucleoprotein complex' 'Ribosomal ribonucleic acid' 'Rootlet of cranial nerve' 'Segment of Brodmann area 1' 'Segment of Brodmann area 27' 'Segment of Brodmann area 29' 'Segment of Brodmann area 33' 'Segment of Brodmann area 45' 'Segment of Brodmann area 48' 'Segment of Brodmann area 49' 'Segment of cortex of gyrus of limbic lobe' 'Segment of cortex of gyrus of temporal lobe' 'Segment of gray matter of medulla oblongata' 'Segment of trunk of anterior tibial artery' 'Set of microtubules' 'Smooth stratified columnar epithelium' 'Spatial association value' 'Subdivision of gigantocellular nucleus' 'Subfascial bursa' 'Superficial lymph node of thorax' 'Synaptic connectivity' 'Tissue cluster' 'Transitional epithelium' 'Transverse process of sacral vertebra' 'Type D cell of duodenum' 'Type D cell of ileum' 'Type D cell of jejunum' 'Variant cervical spinal ganglion' 'Variant thoracic spinal ganglion' 'Vasculature of inframammary part of chest' 'Vasculature of right inframammary part of chest' 'Vertebral arch of sacral segment' 'Zone of cell body' 'Zone of coracobrachialis' 'Zone of external oblique' 'Zone of internal oblique' 'Zone of prevertebral layer of cervical fascia' 'Zone of rectus abdominis' 'Zone of transversus abdominis' 'Zone of trapezius' Bone Euchromatin Fibrocyte Kinetochore Myofilament
Classes with more than 25 subclasses:	3384
Classes with no definition:	82134

Details

Ontology Id	1053
Acronym	FMA
Visibility	Public
BioPortal PURL	http://purl.bioontology.org/ontology/FMA
Status
Format	OWL
Categories	Anatomy
Groups	Unified Medical Language System
Contact	Onard Mejino, mejino@comcast.net
Home Page	http://sig.biostr.washington.edu/projects/fm/
Publications Page	http://sig.biostr.washington.edu/projects/fm/omEditPublications.html
Documentation Page	http://sig.biostr.washington.edu/projects/fm/AboutFM.html
Description	FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. The description of how this OWL version was generated is in "Pushing the Envelope: Challenges in a Frame-Based Representation of Human Anatomy" by N. F. Noy, J. L. Mejino, C. Rosse, M. A. Musen: http://bmir.stanford.edu/publications/view.php/pushing_the_envelope_challenges_in_a_frame_based_representation_of_human_anatomy
License Information	This ontology is made available via the UMLS. Users of all UMLS ontologies must abide by the terms of the UMLS license, available at https://uts.nlm.nih.gov/license.html

Reviews Add your review

Review By sgranite from Project Electrophysiology Ontology on 12/10/2008
Degree Of Formality Documentation And Support Usability Domain Coverage Correctness Quality Of Content

Versions

Version	Release Date	Upload Date	Downloads
3.1	03/03/2010	09/14/2010	Ontology / Diff
3.0	03/03/2009	05/12/2009	Ontology
1.4	01/03/2007	04/27/2009	Ontology

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Foundational Model of Anatomy (subset)

NeuroFMA

Projects Using This Ontology Create new project

Project	Description	People	Institution
Electrophysiology Ontology	The Electrophysiology (EP) Ontology is part of Project 2 of the... The Electrophysiology (EP) Ontology is part of Project 2 of the Cardiovascular Research Grid (CVRG), an NHLBI funded effort to develop a national infrastructure for managing, sharing, and analyzing a broad range of cardiac data. The EP Ontology will contain terms for describing single-channel electrophysiological experiments and data obtained using voltage-clamp, current clamp and fluorescence imaging techniques applied at the cell level and multi-channel fluorescence imaging techniques applied at the cell, tissue and whole heart levels.	Dr. Raimond L. Winslow, Stephen J. Granite Dr. Raimond L. Winslow, Stephen J. Granite	The Johns Hopkins University
Cell line ontology	Cell lines are key experimental models to understand protein in... Cell lines are key experimental models to understand protein interactions and signaling pathways. With a large pool of such data coming from different cell lines of different origin -of normal and -pathological tissues, proper analysis requires segregating data pertaining to specific cell lines. The project envisaged brings together hierarchical trees of organs, mammalian cell lines and diseases in one platform. Certain specific terms from Cell Type (CL) ontology, Foundational Model of Anatomy (FMA) and DOID ontologies are mapped for searchability. Ontology is developed in both OBO and OWL.	Arathi Raghun... Arathi Raghunath, Bharat Bhat, Jignesh Bhate, Usha Mahadevan	Molecular Connections Pvt. Ltd
Influenza Ontology	The Influenza Ontology is an application ontology covering the ... The Influenza Ontology is an application ontology covering the numerous aspects if influenza virus basic research, and surveillance. The influenza ontology extends the Infectious Disease Ontology (IDO).	Burke Squires, Lynn Schriml, Joanne Luciano Burke Squires, Lynn Schriml, Joanne Luciano	UT Southwestern, Univ of Maryland, MITRE
NCBO Resource Index	The NCBO Resource Web service is a system for ontology based a... The NCBO Resource Web service is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data resources related to particular ontology concepts. The annotations are generated using the NCBO Annotator and presented through integration with BioPortal, enabling researchers to search for biomedical resources associated (annotated) with specific ontology terms. The NCBO Resources web service uses a concept recognizer (currently provided by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand these using ontology is_a relations in the ontology. The system's indexing workflow processes the text metadata of diverse resource elements such as gene expression data sets, descriptions of radiology images, clinical trial reports, and PubMed article abstracts to annotate and index them with concepts from appropriate ontologies. Researchers can then search biomedical data sources using ontology concepts.	NCBO NCBO	Stanford University
Plant Ontology	The Plant Ontology is a controlled vocabulary (ontology) that d... The Plant Ontology is a controlled vocabulary (ontology) that describes plant anatomical and morphological structures and growth and developmental stages for all plants. The goal of the PO is to establish a semantic framework for meaningful cross-species queries across gene expression and phenotype datasets from plant genomics and genetics experiments.		Oregon State University
OntoCAT	High level abstraction API (Java/REST/R) for interacting with o... High level abstraction API (Java/REST/R) for interacting with ontology resources including local ontology files in standard OWL and OBO formats (via OWL API) and public ontology repositories: EBI Ontology Lookup Service (OLS) and NCBO BioPortal.	Tomasz Adamus... Tomasz Adamusiak, Helen Parkinson, Natalja Kurbatova, Misha Kapushesky, Morris Swertz	EMBL-EBI, University of Groningen
LogMap	Logic-based and Scalable Ontology Matching. LogMap is a highly ... Logic-based and Scalable Ontology Matching. LogMap is a highly scalable ontology matching system with `built-in' reasoning and diagnosis capabilities. Currently, LogMap is the only matching system that can sucessfully deal with semantically rich ontologies containing tens (and even hundreds) of thousands of classes. Furthermore, LogMap is able to produce a `clean' set of output mappings in many cases. Our experiments with the ontologies NCI, FMA and SNOMED CT confirm that our system can efficiently match even the largest existing bio-medical ontologies.	Ernesto Jimenez Ruiz and Bernardo Cuenca Grau Ernesto Jimenez Ruiz and Bernardo Cuenca Grau	University of Oxford
SKELETOME	The aim of the SKELETOME project is to develop a community-driv... The aim of the SKELETOME project is to develop a community-driven, ontology-based knowledge curation platform for the skeletal dysplasia domain.	Tudor Groza Tudor Groza	School of ITEE, The University of Queensland
Neural ElectroMagnetic Ontologies (NEMO)	NEMO is developing ontologies for representation and integratio... NEMO is developing ontologies for representation and integration of event-related brain potentials (ERPs). To support this work, we are developing an integrated tool environment for storage and management of ERP data, ontologies, and ontology-based markup and analysis of data.	NEMO core (Gw... NEMO core (Gwen Frishkoff, Robert Frank, Paea LePendu, Haishan Liu, Dejing Dou, Allen Malony, Jason Sydes, Nathan Dunn); NEMO ERP Consortium (Gwen Frishkoff, Tim Curran, Dennis Molfese, John Connolly, Kerry Kilborn, Chuck Perfetti)	University of Oregon & Georgia State University
Nomenclature for Anatomic Pathology (NAP)	Unifying Nomenclature for Anatomic Pathology in Italy Unifying Nomenclature for Anatomic Pathology in Italy	Arrigo Bondi Arrigo Bondi	SIAPEC-IAP
OntoMaton	OntoMaton is a google spreadsheet application allowing for onto... OntoMaton is a google spreadsheet application allowing for ontology search and tagging directly within google spreadsheets. More information can be found here: https://github.com/ISA-tools/OntoMaton	ISA team ISA team	Oxford University
BioAssay Ontology	The BioAssay Ontology (BAO) is an NIH-funded project to develop... The BioAssay Ontology (BAO) is an NIH-funded project to develop standard terminologies and a formal, extensible, knowledge-based description of biological assays and assay data (the ontology). Biocuration is a component of the BAO project to systematically annotate biological assays such as those in PubChem with standardized terminology describing assay concepts defined in the ontology. The BAO project also develops software tools to query and explore data sets in the context of the ontology.		University of Miami
SemGen	SemGen is a software tool for automating the modular compositio... SemGen is a software tool for automating the modular composition and decomposition of biosimulation models. It uses BioPortal web services to provide model annotators access to reference ontology terms.	Maxwell Neal, Daniel Cook, John Gennari Maxwell Neal, Daniel Cook, John Gennari	University of Washington
NCBO Annotator	A Web service that tags free text with ontology concepts. NCBO ... A Web service that tags free text with ontology concepts. NCBO uses these Web services to annotate resources in the NCBO Resource Index to create an ontology index of these resources. This Web service can be accessed through BioPortal or used directly in your software. Currently, the annotation workflow is based on syntactic concept recognition (using concept names and synonyms) and on a set of semantic expansion algorithms that leverage the semantics in ontologies (e.g., is_a relations). Our service methodology leverages ontologies to create annotations of raw text and returns them using semantic web standards.	NCBO NCBO	Stanford University
Adverse Event Reporting Ontology (AERO)	The Adverse Event Reporting Ontology (AERO) is an ontology aime... The Adverse Event Reporting Ontology (AERO) is an ontology aimed at providing logical representation of adverse events guidelines, increasing quality and accuracy of reported events.	Melanie Courtot Melanie Courtot

The National Center for Biomedical Ontology is one of the National Centers for Biomedical Computing supported by the NHGRI, the NHLBI, and the NIH Common Fund under grant U54-HG004028.
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