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Re: [OBO-Edit Working Group] Re: User Guide first section
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From: John Day-R. <joh...@ay...> - 2006-04-27 01:11:23
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Hi, Melissa. Sorry to stall this further, but I need to know what filter you're doing so I can reproduce your problem on my end. -John On Apr 25, 2006, at 4:56 PM, Melissa Haendel wrote: > Hi John, please find attached a word file with my edits on the viewing > ontologies section. I still can't access the tracker, so I hope this > will do in the interim. Let me know if there is a better way.... > > thanks, > melissa > > John Day-Richter wrote: >> >> Midori, >> >> Thank you so much for these incredibly helpful notes. Inline comments >> below indicate how I've integrated your advice... >> >> Midori Harris wrote: >> >>> Hi John (et al.), >>> >>> Here (after much delay) are some comments and suggestions for the >>> user >>> guide ... >>> >>> The "What is OBO-Edit?" section is mostly OBO_Edit's illustrious >>> history. I suggest adding a tiny bit more on what it OBO-Edit is, and >>> adding a subheading for the history: >>> >>> OBO-Edit is an application for viewing and editing OBO ontologies. >>> change to ... >>> OBO-Edit is an open source, platform-independent application for >>> viewing and editing OBO ontologies. >>> >>> OBO-Edit is a graph-based tool; its emphasis on the overall graph >>> structure of an ontology provides a friendly interface for >>> biologists, and makes OBO-Edit excellent for the rapid generation >>> of large ontologies focusing on relationships between relatively >>> simple classes. >>> >>> [anything to add on what it is?] >>> >>> add subheading: >>> >>> A brief history of OBO-Edit >>> >>> OBO-Edit began life as GO-Edit, a tool designed exclusively for use >>> in editing the Gene Ontology. [rest of blurb] >>> >> Done. >> >>> "What is an ontology?" needs more on, well, what an ontology is. >>> Also, >>> the first paragraph after the dictionary def could move to the intro >>> to OBO ontologies -- it seems to fit better there. >>> >> I just cut the section on OBO ontologies entirely. I tried to >> integrate it into the "An Introduction to OBO Ontologies" section and >> then realized it was perfectly redundant. >> >>> How about: >>> >>> From dictionary.com: >>> ontology >>> >>> An explicit formal specification of how to represent the objects, >>> concepts and other entities that are assumed to exist in some >>> area of interest and the relationships that hold among them. >>> >>> In other words, ontologies represent domains of knowledge by >>> defining entities within the domain (and the terms used to refer to >>> them) as well as how the entities are related to each other. An >>> ontology thus provides a vocabulary for communicating knowledge >>> about a topic, as well as a computable representation of the >>> underlying reality. >>> >>> Many ontologies, including OBO ontologies, model concepts inmodel >>> concepts in terms of classes (types of entities) and properties >>> (fetures of an entity). Classes are related to each other via >>> properties. >>> >>> Special software (known as a reasoner) can use the network of >>> classes and properties in an ontology to check the ontology for >>> errors, discover the logical implications of existing structures, >>> and suggest new concepts that might be added to the ontology. >>> >>> Keep the blue "Ontology?" box - I like it! >>> >> Done. >> >>> >>> "Getting Started" >>> - important addition: what version of Java is required (obviously of >>> use for the web version, but it should be somewhere - it's very hard >>> to find!) >>> >> I added installation instructions for Java. >> >>> - rest is fine, except correct 'independant' to 'independent' >>> throughout. >>> >> How humiliating. >> >>> "An Introduction to OBO Ontologies" >>> - correct 'analagous' to 'analogous' >>> >> See previous. >> >>> Modest suggestion for the beginnig of the section: >>> >>> OBO-Edit operates on ontologies that conform to the OBO ontology >>> format. The complete specification of the OBO ontology format is >>> available at >>> http://www.godatabase.org/dev/doc/obo_format_spec.html. >>> >>> OBO ontologies are similar to the ontologies specified by a >>> description logic language like OWL or DAML+OIL, albeit >>> simpler. However, [rest of passage] >>> >> Good call. >> >>> Part of this section are tough going for a biologist, tho I suppose >>> that can't be entirely avoided, given the subject matter. >>> >>> This passage in particular confuses me, especially the second >>> sentence: >>> >>> Like classes, properties can be sub-typed. If a property A has an >>> is_a relationship to a another property B, A is a sub-property of >>> B. Any class-level or instance-level relationship over A is also a >>> relationship over B. >>> >>> Maybe an example would help. Also, could the second sentence be >>> changed to 'Any class-level or instance-level relationship of type A >>> is also a relationship of type B.'? (Would that still be accurate?) >>> >> Barry probably won't like it, but I use that kind of terminology >> everywhere else in the guide, so I'm changing it to your suggested >> wording. >> >>> This one also loses me toward the end: >>> >>> These relationships are special because they are applied as >>> instance-level relationships between classes and properties. When >>> we say shoe is_a sneaker, the is_a relationship DOES NOT mean that >>> there is some particular instance of shoe that has an >>> instance-level is_a relationship to a particular instance of >>> sneaker. When we say shoe is_a sneaker, we are creating an >>> instance-level is_a relationship between the classes shoe and >>> sneaker. >>> >>> Does the last sentence mean that we're saying every instance of >>> sneaker is also an instance of shoe ? If so, can we come out and say >>> so? If not, help! because I don't understand. >>> >> No. That's /not /what the passage means. Here's what I'm trying to >> convey... >> >> When you say "finger -part_of-> hand", you're making a statement >> about class AND instances. You're saying that when there's an >> instance of finger ("johns_left_index_finger") it must be an >> instance-level part of some instance of hand ("johns_left_hand"). >> This is true for any user-defined property. >> >> But built in properties like is_a are different. When you say "finger >> -is_a-> digit", you ARE NOT saying that there's an instance of finger >> ("johns_left_index_finger") that somehow has an instance-level is_a >> relationship to an instance of digit ("johns_digit"?? >> "johns_left_index_finger"??). That doesn't really make sense. And the >> reason it doesn't make sense is that OBO-Edit's is_a relationship IS >> ITSELF an instance-level relationship, where OBO-Edit terms are the >> instances being related. >> >> So, do we have a suggestion on how to articulate this better? If not, >> we probably could get away with cutting this section. It addresses >> some fairly arcane points that most users won't care about. >> >>> Finally, these subheadings are empty. Please consider yourself >>> badgered to write some content for them! >>> >>> Symmetry >>> Transitivity >>> Cyclicity >>> Domain & Range >>> Instances >>> Identifiers >>> Obsoletes >>> Meta-Data >>> Namespaces >>> >> Badgering successful. >> >> -John >> >> >> ------------------------------------------------------- >> Using Tomcat but need to do more? Need to support web services, >> security? >> Get stuff done quickly with pre-integrated technology to make your >> job easier >> Download IBM WebSphere Application Server v.1.0.1 based on Apache >> Geronimo >> http://sel.as-us.falkag.net/sel? >> cmd=lnk&kid=120709&bid=263057&dat=121642 >> _______________________________________________ >> Geneontology-oboedit-working-group mailing list >> Gen...@li... >> https://lists.sourceforge.net/lists/listinfo/geneontology-oboedit- >> working-group > > -- > > Melissa Haendel, Ph.D. > > > ZFIN Scientific Curator > > Zebrafish Information Network > > 5291 University of Oregon > > Eugene, OR 97403-5291 > > Phone: (541) 346-5108 > > <viewingontologies.doc> |