Xenopus Anatomy Ontology
Countries that developed this resource United States
Created in 2008
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.
Record updated: July 8, 2019, 9:07 a.m. by The FAIRsharing Team.
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: Before: help|http://www.xenbase.org/geneExpression/static/XpatSearchTips/XpatSearchTips.jsp#Anatomy After: email@example.com help|http://www.xenbase.org/geneExpression/static/XpatSearchTips/XpatSearchTips.jsp#Anatomy Added: firstname.lastname@example.org Removed: 'contactORCID' has been modified: Before: After: 0000-0002-9611-1279 'onto_disciplines' has been modified: Before: Anatomy Life Sciences After: Anatomy Developmental Biology Life Sciences Ontology and Terminology Added: Developmental Biology Ontology and Terminology Removed: 'dataProcesses' has been modified: Before: Download Search Anatomy Search Stages After: Download Search Anatomy Search Stages Ontology release Added: Ontology release Removed: 'contact' has been modified: Before: General Contact After: Erik Segerdell 'contactEmail' has been modified: Before: email@example.com After: firstname.lastname@example.org 'grants' has been modified: Before: P41 HD064556 After: P41 HD064556 R01HD045776-03 Added: R01HD045776-03 Removed: 'miriam_id' has been modified: Before: None After:
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.
No XSD schemas defined
Conditions of UseApplies to: Data use
|Ontology release||No link recorded|
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
No guidelines defined
Models and Formats
No syntax standards defined
No identifier schema standards defined
No metrics standards defined
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.
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 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.
This record is not implemented by any policy.
This record is maintained by xenbase
National Institutes of Health (NIH), Bethesda, MD, USA (Government body)
Xenbase administrators (Consortium)
P41 HD064556 (National Institute of Child Health and Human Development (NICHD), Rockville, MD, USA)
R01HD045776-03 (National Institutes of Health (NIH), Bethesda, MD, USA)