Ontology Domain Concept Relationships
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The document discusses an ontology for concepts and relationships within the domain of hymenoptera (bees, ants, wasps). It describes how concepts are represented as classes which can have many labels or synonyms. An example is provided of the class "external male genitalia" and its various labels. Statistics are provided on terms extracted from literature to expand an existing hymenoptera ontology.
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Ontology Domain Concept Relationships
- 3. Formal representation of concepts within a domain and the relationships between those concepts. ontology ≠ ontogeny Ontology domain = hymenoptera concept = class (an real anatomical thing) label = words used to represent anatomical things ****a class can contain many labels***
- 4. male genitalia phallus parameres copulatoria genital capsule genital armature phallic apparatus genital apparatus armatura genitalis genital appendage copulatory apparatus external genital organ male copulatory organ www.hymao.org a class can have many labels
- 5. www.hymao.org this real thing is a class male genitalia phallus parameres copulatoria genital capsule genital armature phallic apparatus genital apparatus armatura genitalis genital appendage copulatory apparatus external genital organ male copulatory organ a class can have many labels
- 6. male genitalia phallus parameres copulatoria genital capsule genital armature phallic apparatus genital apparatus armatura genitalis genital appendage copulatory apparatus external genital organ male copulatory organ www.hymao.org a class can have many labels this real thing is a class these are all labels
- 7. [Term] id: HAO:0000312 name: external male genitalia def: "The compound organ that is involved in coupling with the female genitalia and with the intromission of spermatozoa and seminal fluid." [HAO:im] synonym: "armatura genitalis" [] synonym: "copulatoria" [] synonym: "copulatory apparatus" [] synonym: "genital apparatus" [] synonym: "genital appendage" [] synonym: "genital armature" [] synonym: "genital capsule" [] synonym: "genital organ" [] synonym: "male copulatory organ" [] synonym: "parameres" [] synonym: "phallic apparatus" [] synonym: "phallus" [] relationship: part_of HAO:0000505 ! male genitalia is_a: HAO:0000024 ! compound organ [Term] id: HAO:0000313 name: external paramera def: "The anatomical cluster that is composed of the gonostipites and volsellae." [HAO:im] relationship: part_of HAO:0000312 ! external male genitalia is_a: HAO:0000041 ! anatomical cluster Open Biomedical Ontologies (OBO)
- 8. Nasonia spp. >50 mutants implications: vehicle to integrate research
- 9. process mx http://purl.oclc.org/NET/mx-database MX
- 10. process mx software (development) community feedback (Hymenoptera, ontology & computer science) exposure
- 11. 2,682 labels 1,382 classes 865 references 3058 times referenced 1201 from just a few papers
- 12. Term extraction from BHL 353 JHR
- 14. results highest number > 50 vein (465) wing (282) cell (219) wing vein (114)
- 15. results carina (187) tergum (183) tergites (128) propodeum (83) sternum (65) highest number > 50
- 16. results smooth (94) small (87) short (85) highest number > 50
- 17. results glossa (72) highest number > 50
- 18. results cell (219) area (116) base (84) apex (76) body (71) highest number > 50
Notes de l'éditeur
- 10 minute talk for the 2009 Entomological Society of America meeting in Indianapolis, Indiana.
- >145,000 species described for the hymenoptera. As a community we have a lexicon to describe the structures we wish to explain; a lexicon of word labels to convey information about the organisms we are interested. Many of these labels are in the glossaries of out texts and keys (print form and online), journal publications and primarily locked in the heads of those who study hymenoptera. From the more than 200 members of the International Society of Hymenopterists (http://hymenopterists.org) and the many other researchers that work with bees, wasps, sawflies and ants.
- Our goal is to organize these words using a set of rules laid down by the ontology community in order to create a document (an ontology) that can be machine reasoned. An ontology by definition is a “Formal representation of concepts within a domain and the relationships between those concepts.” For us the domain is hymenoptera, the concepts are real anatomical things, and labels are the words we use to represent the anatomical things. The Hymenoptera Anatomy Ontology (HAO) uses is_a and part_of relationships to explain relationships between classes. These relationships are not discussed in this presentation but there are important implications with these relationships; particularly how relationships between other classes may be inferred.
- A class can have many labels: an example.
- The complex structure that male hymenopterans use to deliver sperm to the female has been referred to by at least 13 names in English. The actual real thing itself is what we are trying to describe, this is the class.
- Every class may have multiple labels. Each of these are words used to describe the class. The important point here is that the Hymenoptera Anatomy Ontology (HAO) is interested in capturing the information about classes and labels, without having a preference or preferred term!
- In practical sense what we are producing is a text file and this text file is exposed on the Web using BioPortal (http://bioportal.bioontology.org) and Obo Foundry (http://www.obofoundry.org). The file is either in OBO format (displayed here) or OWL format, which is XML. This text file is generated by a database and not hand written. Here we see outlined in yellow one class from the ontology and some of the components required to be a valid ontology. Each class must have a unique id + namespace. The classes are named and defined. All of the labels are listed in the class. And finally the relationships between this class and other classes in the ontology are listed.
- A logical collection of the lexicon has many implications for research particularly in our web 2.0 world; helping to create intelligent interactions between biodiversity initiatives and publications. The implications are huge. Imagine a more intuitive search mechanism where when a researcher is looking for information about a label and information can be returned for all labels in a given class. Also we plan on illustrating our classes with images, visually defining the lexicon. Essentially creating an logically controlled illustrated glossary of the hymenoptera lexicon, greatly benefiting future hymenoptera researchers and students.
- The software we are using to construct the ontology is MX (http://hymenoptera.tamu.edu/wiki). MX is a series of online tools for revisionary systematics and taxonomy. The ontology component is only one portion of the MX software and database. We are using our own software for a number of reasons. Primarily in order to construct new tools for working with the ontology we need a system that can be rapidly modified. Also, besides the HAO, we are capturing other information in the database including reference, specimen and matrix based information. This scope of information, along with the association with the HAO we hope will allow us to build exciting tools for systematic and taxonomic research.
- The process is iterative. We produce an ontology from the MX software. This ontology is then exposed on the web via BIoPortal (http://bioportal.bioontology.org) and OBO Foundry (http://www.obofoundry.org). Multiple versions of the ontology are kept and exposed through these resources. From this exposure we gather feedback from the Hymenoptera, ontology and computer science communities. From this feedback we modify the software, adding new tools and modifying the HAO classes in order to create a more robust HAO.
- At the time of this presentation we have over 1000 classes in the HAO. Associated with those classes are nearly 3000 labels. Attached to these classes are 865 references used to justify the our decisions regarding definitions, labels and classes themselves. From these 3000 references over 1000 of them have come from very few publications. There are some naturally rich glossaries and dictionaries that we expect to reference extensively but it made us wonder how many labels and classes might be elucidated from examining journal articles in the literature, without perceiving of these articles as being particularly fruitful sources for the HAO.
- Thanks to the International Society of Hymenopterists (http://www.hymenopterists.org) contributing all of its articles except the past two years to the Biodiversity Heritage Library (http://www.biodiversitylibrary.org) we are able to access OCR from these documents using a novel workflow. We gathered the reference information and imported it into MX by article using Google Scholar searches and export as endnote functionality. These were collected using the Firefox plugin Zotero (http://www.zotero.org). Once the references were in MX we added the OCR export from BHL to the MX database. MX contains a proofing tool to help us discover new terms. The proofer first matches on terms presently in the database and highlights them in the text. Than it presents unique combinations of words for review as potential new terms. These combinations are reviewed by a person and added in batch to the database. The proofer tool underwent significant improvement during the initial examination of articles but human skill and work is still substantial to this process. Human effort is necessary to make the decisions between a potential new database addition and just random word associations.
- We managed to parse 23 papers with the proofing tool. From these 23 terms we added 347 new objects to the database. 137 of these objects are PATO labels. PATO, or ontology of phenotypic qualities, is a separate project from the HAO. However, we hope to incorporate adjectives and qualifiers often used in hymenoptera morphology into PATO so we can begin to make more complex statements about characters. Before we began this exercise we were very conservative about which PATO terms we added to the database but through the process it became apparent that we will need to add a large number of terms to capture the phenotypic qualities associated with hymenoptera morphology. The large number of PATO terms added at this time is due to a change in ideology on our part to be more inclusive about which terms we will include. 210 new labels (and potentially new classes) were added to MX from the 23 papers. Many of these will be defined and incorporated into the HAO. In the 23 papers we found over a thousand distinct labels and almost 9000 occurrences of those labels. About half of these occurred more than 50 times.
- As preliminary results we can say that hymenopterists love to talk about wings and wing venation.
- In regards to structures on the body we as a community often speak about carina on the tergum or individual tergites.
- We like smooth, small and short things.
- There were 72 occurrences of the label glossa, mostly from Mitchener. Therefore we can possibly conclude it very well maybe his favorite character system?
- Some interesting challenges are elucidated through these data as well. Terms like cell may represent multiple classes. For example, a cell could be a wing cell, or a cell in reference to a population of organisms. There are many of these terms in the ontology that will need to be identified.
- And for the future? First we need to parse the rest of the 353 Journal of Hymenoptera Research Articles. One primary reason we are using web based software is to allow individuals anywhere geographically to contribute to the data. So if anyone would like to help proof one or more of these articles please let us know! We will need to define and examine all the new classes and labels added to the database. We continue to reevaluate our workflow, improving the proofer and trying to improve our tie in to the Biodiversity Heritage Library.
- Much more information including our HAO-TO is found at www.hymao.org.