Transforming Systematics

From HAO Wiki

Systematic research can be significantly transformed when a robust ontology provides a foundation for the research of a broader community. Our tools will facilitate the integration of ontologies into systematic research, in particular through linkages to taxonomic descriptions and the hypotheses of homology that underlie phylogenetic research. By providing a framework that allows researches to vet their work against an ontology we thereby ensue that a maximum number of semantic linkages occur prior to their work being exposed to the larger scientific community. By increasing the probability of linkages among research we inherently accelerate the possibility of cross-discipline discovery, i.e. we increase the potential for truly transformative discoveries.

We will develop a set of RESTful web services (API) that expose the functionality of the ontology database to web applications. This API allows any Web developer to make use of our core application. In addition, three web applications will be developed, each of which employs and illustrates aspects of the API:

1. A digital atlas of Hymenoptera anatomy. We will expand the Hymenoptera Glossary to more fully take advantage of the tie-ins illustrations used on Morphbank and to include a suite of additional features that allow users to customized their own atlas, for example by selecting a group of terms or images. Personalized slices of the atlas will be useful to broad array of users, for example educators that teach anatomy, teams of monographers that require sets of commonly referenced or even unique terms, and non-experts who need specialized sets of characters to diagnose problematic taxa (e.g., USDA inspectors that need to identify ants at ports and borders). We will also enable users to download a world-list dictionary to install in their word processors.
2. A syntax highlighting browser plug-in. The plug-in will include a toolbar with straightforward functionality that will allow users to syntax-highlight the text on a given page using the HAO. Clicking on the highlighted text will take the user to the atlas, or provide other context-sensitive responses. The plug-in toolbar/sidebar will include a search interface to the HO and allow users to quickly check the definition of a given word.
3. An ontology integration wizard for descriptive terminology. The wizard will greatly extend the existing functionality prototyped in the ontology proofing tool. A user starts by pasting in or uploading a file containing descriptive text (for example taxon or phylogenetic character descriptions). Subsequent functionality allows syntax highlighting that will return references for terms in the HO (or other ontologies integrated into the HAO DB, e.g. PATO, spatial ontology, units of measurement). Functionality for making corrections, exchanging synonyms, removing homonyms, and in place review against available images will be included. Once the text in question has been vetted against the ontology to the users satisfaction s/he will be able to generate various markups of the text, including a publication ready hyperlinked version (for journals that allow embedded links) which ties text directly to the HO DB. Other possible markups will include XML, HTML, or SDD, allowing users to cut and paste their marked-up text to their personal websites or applications. Options will include the ability to send the text in question directly to the HAO team at which point it will be queued for review against and possible inclusion in the HAO. An opt-in personalized option will allow users to allow their text to be archived for further comparison to the HAO. This corpus of data will be mined for missing terms, and possible relationships among terms.

Our applications will be tested with real-life data throughout the course of the project, and we have partnered with several ongoing efforts in this regard. In close conjunction with AmphibAnat we will both share our effort and adopt their work where possible, synergistically improving both efforts.