Xenopus Anatomy Ontology

Abbreviation: XAO

General Information

The Xenopus Anatomical Ontology (XAO) describes Xenopus anatomy and embryological development using a 'controlled vocabulary' of anatomy terms that are organized in an hierarchy with a graphical structure. XAO terms describe gene expression, and the XAO is constantly being updated in response to the latest published Xenopus research.

Homepage http://www.xenbase.org/anatomy/xao.do?method=display

Countries that developed this resource United States

Created in 2008

Taxonomic range

Xenopus

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: XAO; Xenopus Anatomy Ontology; DOI: https://doi.org/10.25504/FAIRsharing.17zapb; Last edited: Aug. 13, 2019, 3:59 p.m.; Last accessed: Oct 22 2020 1:50 p.m.

This record is maintained by xenbase

Record updated: July 8, 2019, 9:07 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.17zapb' by 'The FAIRsharing Team' at 09:07, 08 Jul 2019 (approved):

	'onto_domains' has been modified:
		Before:
			morphology
			structure
		After:
			life cycle
			life cycle stage
			morphology
			structure
		Added:
			life cycle
			life cycle stage
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.17zapb' by 'The FAIRsharing Team' at 09:02, 08 Jul 2019 (approved):

	'organizations' has been modified:
		Before:
			Xenbase administrators|http://www.xenbase.org/entry|Maintains
			National Institute of Child Health and Human Development (NICHD), Rockville, MD, USA|https://www.nichd.nih.gov/Pages/index.aspx|Funds
		After:
			National Institute of Child Health and Human Development (NICHD), Rockville, MD, USA|https://www.nichd.nih.gov/Pages/index.aspx|Funds
			Xenbase administrators|http://www.xenbase.org/entry|Maintains
			National Institutes of Health (NIH), Bethesda, MD, USA|http://www.nih.gov|Funds
		Added:
			National Institutes of Health (NIH), Bethesda, MD, USA|http://www.nih.gov|Funds
		Removed:

	'supportLinks' has been modified:
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			help|http://www.xenbase.org/geneExpression/static/XpatSearchTips/XpatSearchTips.jsp#Anatomy
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			email|xenbase@ucalgary.ca
			help|http://www.xenbase.org/geneExpression/static/XpatSearchTips/XpatSearchTips.jsp#Anatomy
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			email|xenbase@ucalgary.ca
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	'contactORCID' has been modified:
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		After: 0000-0002-9611-1279

	'onto_disciplines' has been modified:
		Before:
			Anatomy
			Life Sciences
		After:
			Anatomy
			Developmental Biology
			Life Sciences
			Ontology and Terminology
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			Developmental Biology
			Ontology and Terminology
		Removed:

	'dataProcesses' has been modified:
		Before:
			Download
			Search Anatomy
			Search Stages
		After:
			Download
			Search Anatomy
			Search Stages
			Ontology release
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			Ontology release
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	'contact' has been modified:
		Before: General Contact
		After: Erik Segerdell

	'contactEmail' has been modified:
		Before: xenbase@ucalgary.ca
		After: segerdel@ohsu.edu

	'grants' has been modified:
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			P41 HD064556
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			P41 HD064556
			R01HD045776-03
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			R01HD045776-03
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	'miriam_id' has been modified:
		Before: None
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Edits to 'https://fairsharing.org/FAIRsharing.17zapb' by 'The FAIRsharing Team' at 22:44, 30 Nov 2016 (approved):

	'description' has been modified:
		Before: The Xenopus Anatomical Ontology (XAO) describes Xenopus anatomy and embryological development using a 'controlled vocabulary' of anatomy terms that are organized in an hierarchy with a graphical structure. XAO terms describe gene expression, and the XAO is constantly being updated in response to the latest published Xenopus research. The XAO contains 1000's of terms and relationships. Each anatomical system (eg; central nervous system|alimentary/biliary system)|tissue and structure (eg; neural fold|mesoderm|blastpore) and many cell types (eg.|clilated epidermal cell|migrating neural crest cell) are separate terms; each term is fully defined and related to other terms by is_a|part_of |develops_from and develops_into relationships. All growth/life cycles stages (eg blastula|gastrula|tadpole) and Nieuwkoop & Faber stages (NF stages) are also XAO terms (e.g.|gastrula stages include NF stage 10 to NF stage 12.5). This allows the timing of anatomical development to be indicated by starts_during and ends_during relationships with NF stages.
		After: The Xenopus Anatomical Ontology (XAO) describes Xenopus anatomy and embryological development using a 'controlled vocabulary' of anatomy terms that are organized in an hierarchy with a graphical structure. XAO terms describe gene expression, and the XAO is constantly being updated in response to the latest published Xenopus research.

Support

General

support email	General contact
help	http://www.xenbase.org/geneExpression/st ...

Additional Information

Contact

Erik Segerdell ORCID

External Links

Bioportal	http://bioportal.bioontology.org/ontologies/XAO
OBO	http://obofoundry.org/ontology/xao.html

Tools

No tools defined

Schemas

No XSD schemas defined

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Creative Commons Attribution 3.0 Unported (CC BY 3.0)

Data Release

Ontology release

No link recorded

Data Access

Download	http://www.xenbase.org/anatomy/downloadXao.do?method=display&tabId=1
Search Anatomy	http://www.xenbase.org/anatomy/anatomy.do?method=display&tabId=2
Search Stages	http://www.xenbase.org/anatomy/stage.do?method=display&tabId=3

Publications

Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase.

Segerdell E,Ponferrada VG,James-Zorn C,Burns KA,Fortriede JD,Dahdul WM,Vize PD,Zorn AM
J Biomed Semantics 2013

View Paper (PubMed) View Publication

An ontology for Xenopus anatomy and development.

Segerdell E,Bowes JB,Pollet N,Vize PD
BMC Dev Biol 2008

View Paper (PubMed) View Publication

XAO Ontology Display

View in BioPortal.

Disclaimer: This widget assumes the availability of the ontology resources in the NCBO BioPortal.

View in OBO Foundry.

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

UBER anatomy ONtology

Models and Formats

No syntax standards defined

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases (4)

Bgee DataBase for Gene Expression Evolution
Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). Bgee is based exclusively on curated "normal", healthy, expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of normal gene expression. Bgee produces calls of presence/absence of expression, and of differential over-/under-expression, integrated along with information of gene orthology, and of homology between organs. This allows comparisons of expression patterns between species.

Xenopus laevis and tropicalis biology and genomics resource
Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. It includes gene expression patterns that incorporate image data from the literature, large scale screens and community submissions.

OBO Foundry
The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. To achieve this, OBO Foundry participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations, based on ontology models that work well, such as the Gene Ontology (GO). The OBO Foundry is overseen by an Operations Committee with Editorial, Technical and Outreach working groups.

Domain-centric GO
Domain-centric GO provides associations between ontological terms and protein domains at the superfamily and family levels. Some functional units consist of more than one domain acting together or acting at an interface between domains; therefore, ontological terms associated with pairs of domains, triplets and longer supra-domains are also provided.

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by xenbase

Funds

National Institute of Child Health and Human Development (NICHD), Rockville, MD, USA (Government body)
National Institutes of Health (NIH), Bethesda, MD, USA (Government body)

Maintains

Xenbase administrators (Consortium)

Grant Number(s)

P41 HD064556 (National Institute of Child Health and Human Development (NICHD), Rockville, MD, USA)
R01HD045776-03 (National Institutes of Health (NIH), Bethesda, MD, USA)

Xenopus Anatomy Ontology

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