HAO to

From HAO Wiki

How do I contribute to the HAO?

See How do I contribute?

How do I utilize the HAO?

• Much of the core content is available at the Hymenoptera Anatomy Ontology Portal, the primary public interface of the underlying HAO database.
• There are a series of use cases being outlined.

How do I cite the HAO?

Original publication

The HAO was introduced in this publication:

 Yoder MJ, Mikó I, Seltmann KC, Bertone MA, Deans AR, 2010 A Gross Anatomy Ontology for Hymenoptera. PLoS ONE 5(12): e15991. doi:10.1371/journal.pone.0015991 

The HAO homepages (these pages)

 Hymenoptera Anatomy Consortium. The Hymenoptera Anatomy Ontology Hompage: Accessed on some time. Available at http://purl.oclc.org/NET/hymontology

In taxonomic or other descriptive text

Note that methods for including linkages to ontologies in published papers are in their infancy. Please anticipate that the following recommendations will evolve.

In a materials and methods section

It's important that the reader understand the role that links provided in digital descriptions are playing- are they simply to enhance the paper for the reader or to provide semantic enhancements that are digitally consumed? Referencing HAO concepts is analogous to providing a GenBank number in your paper. That Genbank identifier can be used in a wide range of different portals to return the exact sequence being referenced, or utilized in other manners (e.g. in a Blast search). The Hymglossary ([1]) is only one such portal with which a HAO id can be used, for example others include Bioportal (http://bioportal.bioontology.org/) and Ontobee (http://www.ontobee.org/browser/index.php?o=HAO). Providing a HAO concept id (e.g. HAO:0123456) in the form of a URI (e.g. http://purl.obolibrary.org/obo/HAO_0000124) will enable additional linkages to ultimately be realized through software based parsing and reasoning. These URIs present resolve to the preferred OBO Foundry portal, Ontobee.

To reference the HAO's concepts in a taxonomic paper some discussion of the role of the links might be relevant to readers, the following is provided as an example and can be reproduced or modified as necessary:

Creating links to the HAO's web-based resources in documents

References to particular concepts (structures/anatomy) in the HAO can be made independent of the labels used for those concepts. This allows users to use whatever label/term for a particular feature/character while also linking to a definition which they feels best defines what they want to convey. At present there are two standard ways to link text:

1. As a OBO Foundry URI (e.g. http://purl.obolibrary.org/obo/HAO_0000124)
   • Pros:
     • Ensures the greatest potential for long term stability of the hyperlink
     • Can be resolved in multiple contexts to provide additional human and machine based metadata
     • Is a URI in web-standard ontology format, see OWL and therefor inherently "plays nice" with other ontologies (i.e. is applicable to a very large web community)
     • Resolves to a HAO endorsed "homepage" for the concept in question.
   • Cons:
     • <TODO - CHECK RE DIFFERENTIALLY RESOLVING URIS>
2. As a Hymenoptera Anatomy Ontology API link (e.g. http://api.hymao.org/api/ontology/ontology_class/HAO_0000124), see API documentation here
   • Pros:
     • Can resolve to a JSON result (e.g. simple machine-parse-able metadata) by further appending '.json', or to HTML
   • Cons:
     • The link resolves to a result that is largely intended for machine parsing, i.e. no nicely human readable result (images, hyperlinks) is returned.

Including links to concepts in TaxPub or similar markup

to do

How do I find technical details on the HAO and OWL?

• The OWL generating script is here at github.