Foundational Model of Anatomy (FMA) Content Characterization

Harold Solbrig
2005-03-15

II. Core Content Characterization

The following attributes of the content characterization will be supplied by XMDR staff.

Attributes marked with an asterisk (*) are considered mandatory.

Title*

The Foundational Model of Anatomy

Acronym

FMA

One of the following (Web page(s), Identifier, or Contact Information) is mandatory:

Web page(s)

http://sig.biostr.washington.edu/projects/fm/

Inclusion Rationale*

The Foundational Model of Anatomy is a rich, detailed and principaled organization of structural anatomy. It has the promise of becoming the core anatomy resource for many domains and uses, and will also provide a good test case as a highly structured, complex ontology.

Subject*

biological, biomedical, medical or healthcare

Kind of Metadata*

Classification/Categorization Schemes and Taxonomies

Ontologies

Size statistics(estimated)*

Approximately 75,000 concepts, 60 relations, 290,000 edges

Initial Submitter*

Harold Solbrig

Date of Initial Survey*

2004-12-05

III. Supplementary Content Characterization

The following attributes of the content characterization will be completed by XMDR staff. These attributes will be collected for those content collections which are considered to be high priority for inclusion in the prototype.

Attributes marked with an asterisk (*) are considered mandatory.

Date*

2004-12-05

Creator

Cornelius Rosse, M.D., D.Sc., University of Washington Department of Biological Structure

Publisher*

UW TechTransfer Digital Ventures

Description*

The Digital Anatomist Foundational Model (FMA) is an evolving computer-based knowledge source for bioinformatics; it is concerned with the representation of concepts and relationships necessary for the symbolic modeling of the structure of the human body in a form that is understandable to humans and is also navigable by machine-based systems. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. The Digital Anatomist Foundational Model is one of the information resources integrated in the distributed framework of the Anatomy Information System developed and maintained by the Structural Informatics Group at the University of Washington.

Language(s)*

English

Latin

Graph-theoretic Classification*

Format / Schemas(s)*

Protege / FMA model

LexGrid format is available through Mayo Clinic

Draft OWL version is (possibly) available through NLM

Media / Download*

Is the metadata resource available for download? What are the principal / mirror download sites ? What media types (CDROM, DVD, ...) are available (if any)?

Constraint Specifications

Does the metadata resource include constraints? What kinds of constraints (keys, foreign keys, ....)? How are constraints specified (SQL, logic, RuleML, SWRL, Object Constraint Language, ...) ?

Protocol(s)

What protocols does the metadata publisher support for download, other access, e.g., FTP, HTTP, REST, SOAP, UDDI, LDAP, etc.

Licensing Issues*

Open source, public domain, academic use, proprietary license, .... License agreement required ? Cost of license? Can content be redistributed or posted to the web?

Export restrictions

Restrictions on export / distribution ?

Subsets

Is there some subset of the metadata resource which would be of interest? Can we request / extract / query this subset for the originating site or will we have to obtain the complete metadata resource content and then perform the subset extraction query processing on our system?

Versions, Updates

What is the current version number of the metadata resource? How often is the metadata resource updated? How are updates named / distributed / propagated ?

Documentation

What documentation is available? Where / how to obtain documentation ? Format of documentation ?

Character Set Encoding*

Is the data set encoded in ASCII, Unicode (and if so what character encoding UTF-8, UTF-16, ...), or other?

Measurement units

What system of measurement units (e.g., SI, cgs, US customary, ... ) is used (if any)? How are they encoded ?

Dataset / Standards Dependencies

Indicate any dependencies of this metadata resource on other metadata resources or standards, e.g., country codes, terminologies, chemical or biological nomenclature standards, etc.

Related Datasets

Other similar or related metadata resources.

Software tools

What software tools are available to parse, load, convert, browse, edit, .... this metadata resource (type)?

Audience(s)

Who is the primary intended audience for this data set? Expert researchers, DBAs, scientific users, agency staffers, librarians, statisticians, teachers, general public, college students, high school students, ...

Citation

How should the metadata resource be cited in publications, etc. ? Note that the preferred bibliographic citation is often a publication rather than the web site for a resource.

Surveyor*

Person who filled out this section of the survey for this metadata resource. Contact info also.

Date of Survey*

Date this survey was completed / updated for this metadata resource.

IV. Content Characterization by XMDR Staff

The following data elements are to be supplied by XMDR project staff/collaborators.

Attributes marked with an asterisk (*) are considered mandatory.

XMDR Participant Expertise

Names of persons (if any) on XMDR project (and contact info) who are familiar with this data set. XMDR participant organizations who have copies of this metadata resource.

XMDR Evaluator*

Names of persons on XMDR project (and contact info) who evaluated this metadata resource for inclusion (e.g., if the content survey was completed by someone at the content repository).

Inclusion Priority*

Priority suggested for acquisition and ingestion of this metadata resource.