From pj37 at cornell.edu Wed Jan 9 14:05:26 2008 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 09 Jan 2008 14:05:26 -0500 Subject: [Po-dev] International PAG Ontology Workshop 14 January 2008 Message-ID: <47851AF6.8080403@cornell.edu> Dear All, If you are attending the 16th International Plant and Animal Genome meeting to be held in San Diego (USA), everyone is cordially invited to attend the ?Biological Ontologies and Applications? workshop that is scheduled for Monday Afternoon, 14 January 2008 12:50 pm - 3:00 pm. We have a great panel of talks scheduled for this year's workshop, and look forward to see you at the meeting. Thanks Pankaj http://intl-pag.org/16/16-ontology.html Monday Afternoon, 14 January 2008 --- 12:50 pm - 3:00 pm Biological Ontologies and Applications - Royal Palm Salon 1, 2, and 3 Organizer: Pankaj Jaiswal,Cornell University (pj37 at cornell.edu) Workshop Background: The use of various ontologies for biology has been clearly demonstrated in several biological domains e.g., Gene Ontology and Plant Ontology. An Ontology is a common, structured and controlled vocabulary for describing the concepts that exist in an area of knowledge and the relationships that exist between them. Over the last few years a number of ontologies have been developed and implemented for use in the biological databases. However, among the researchers, the enthusiasm for ontologies has been accompanied by a general lack of awareness of what exactly ontologies are and how to use them. In this workshop we are trying to promote awareness and interaction among the researchers (audiences) and the developers of various ontology and/or those developing computational tools for using these ontologies in large/small scale analysis of genomics and genetics datasets. Useful link: OBO Foundry Ontologies Speakers: 12:50pm Michael Ashburner, Department of Genetics, University of Cambridge, UK (ma11 at gen.cam.ac.uk) "GAZ an ENVO: Two new ontologies to help tame data." 1:20pm Bjoern Peters, La Jolla Institute for Allergy and Immunology, USA (bpeters at liai.org) "OBI: Ontology for Biomedical Investigations" 1:45pm Ken Ichiro Fukuda, National Institute of Advanced Industrial Science and Technology, Japan (fukuda-cbrc at aist.go.jp) "Inoh Pathway Event Ontology" 2:10pm Jayesh Pandey, Dept. of Computer Science, Purdue University, USA (jpandey at cs.purdue.edu) "Functional Characterization Of Pathways In Interaction Networks" 2:35pm Neil Sarkar, Encyclopedia of Life, Marine Biological Laboratory, USA (sarkar at mbl.edu) "Towards Developing Practical Taxonomic Ontologies" From cwt6 at cornell.edu Thu Jan 10 11:50:13 2008 From: cwt6 at cornell.edu (Chih-Wei Tung) Date: Thu, 10 Jan 2008 11:50:13 -0500 Subject: [Po-dev] Plant Ontology Computer Demo in PAGXV, 13 January 2008 Message-ID: Dear colleagues, We are pleased to inform you that Plant Ontology Consortium will host a 20-minutes computer demo in Plant & Animal Genome XV (PAGXV), San Diego, CA. http://www.intl-pag.org/16/16-demos.html Title: The Plant Ontology Database: A Community Resource for Plant Structure and Developmental Stages Controlled Vocabulary and Annotations Time: January 13, 5:35pm-5:55pm Place: California Room, Town&Country Convention Center, San Diego, CA Poster number: P931 We look forward to meeting you! If you are not attending the conference, please feel free to browse/download our poster at http:// ascus.plbr.cornell.edu/~gramene/poc/PAG2008 Thank you, Chih-Wei Tung Plant Ontology Consortium Cornell University Ithaca, NY 14850 -------------- next part -------------- An HTML attachment was scrubbed... URL: From schober at ebi.ac.uk Wed Jan 16 06:04:31 2008 From: schober at ebi.ac.uk (Daniel Schober) Date: Wed, 16 Jan 2008 11:04:31 +0000 Subject: [Po-dev] Shaping OBO Foundry naming conventions - survey: input sollicited In-Reply-To: <4786114B.2030706@ebi.ac.uk> References: <4786114B.2030706@ebi.ac.uk> Message-ID: <478DE4BF.1040404@ebi.ac.uk> Dear Plant Ontology curators. /[ This email is being sent at the request of the OBO Foundry coordinators Barry Smith, Suzi Lewis, Chris Mungall and Michael Ashburner]/ I am approaching you regarding your role as an editor/curator of the following ontologies: *Plant growth and developmental stage , http://www.obofoundry.org/cgi-bin/detail.cgi?id=po_temporal Plant structure , http://www.obofoundry.org/cgi-bin/detail.cgi?id=po_anatomy* This is an opportunity for you and your ontology community to *help OBO Foundry** shape **guidelines for naming conventions*. I would appreciate *your input to our survey* on your current practice in naming (labeling) entities within your ontology. The questionnaire is copied below and it is also available at the OBO Foundry wiki http://obofoundry.org/wiki/index.php/Naming Please, fill out the attached *questionnaire *and send it back to me, or alternatively let me know if you are available for a *phone *or *skype interview *and your contact details. The first phase of the survey has been completed and we have already collected answers from* 34 *ontologies! This second and last part of the survey will be closed by Feb 8th and results posted at the OBO Foundry wiki page. If you have any question, please don't hesitate to contact me. Thanks in advance for your reply! Best regards, Daniel Schober * *** The OBO Foundry paper is out in Nature Biotechnology http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf ***** _naming conventions - SURVEY_ Scope The overall goals of this survey are twofold: 1. to evaluate the current practice in naming entities within the OBO ontology working groups 2. to move towards a common set of naming convention for the OBO Foundy Further details on the rationale for this survey can be found in Schober /et al/. 2007, "Towards naming conventions for use in controlled vocabulary and ontology engineering", _http://bio-ontologies.org.uk/download/Bio-Ontologies2007.pdf_, pages 29-32. Results Any questions as well as the completed questionnaires should be sent to Daniel Schober (schober at ebi.ac.uk). The outcome will be posted on the OBO Foundry wiki pages (http://obofoundry.org/wiki/index.php/Naming) and all participants will get notified accordingly. // Questionnaire _1. Questions on your ontology and its engineering and maintenance process_ *1.1 *Are you and your co-workers familiar with the OBO Foundry principles (http://www.obofoundry.org/crit.shtml)? *1.2* If yours in an OBO Foundry ontology, have you started implementing these principles and aligned your development process accordingly? *1.3* Is work on your ontology closely associated with the need to manage and formulate queries about a specific body of data? If so, can you specify the type of data? This question refers to the instance level and annotated data bodies. Is the ontology developed in collaboration with the maintenance of a database or collection of databases (as the GO is developed in collaboration with UniProt and with various MOD databases)? *1.4* Which ontology editor tool(s) do you use to build and manage your ontology? *1.5 *Please illustrate the editing process, i.e. is your ontology developed in a centralised or distributed manner? In both cases, please, state the number of people directly handling and editing the ontology file and if they are physically distributed or if they are located in one spot. *1.6* Do you introduce special /helper classes/ or /bins/, that refer to metadata to facilitate the engineering process? If yes, please describe them and explain how do you indicate their special status? Examples are 'obsolete classes', 'imported classes', 'deleted classes'. _2. General questions on your current practice in naming entities and their documentation_ *2.1* Have you developed naming conventions within your ontology community? If yes, please specify how these are formulated, e.g. as a specific, standalone document or as part of other documentation and where these are available, e.g. provide URL. *2.2 *(If your answer to 2.1 is positive) Which entities are tackled by your naming conventions? Some examples are provided below, add if required: * class names * relation names, e.g. colour vs has_colour vs colour_of * instance names * the name of the ontology, its versions, namespaces and term IDs *2.3* (If your answer to 2.1 is negative) Have you re-used existing naming conventions from other ontology groups? For example have you applied the GO editor style guide or conventions from other sources, e.g. ontology tutorials or guidelines from standardization bodies such as ISO? _3. Questions on the implementation of names_ *3.1 *Which of the following categories of names (or name types) do you record in your ontology and which one do you anticipate such common naming conventions are useful for?// Some examples are provided below, add if required:// ? preferred name ? short name or display name ? formal name ? synonym ? foreign language translations ? broader or narrower term *3.2* (If applicable) Which ontology language idioms do you use to capture the categories of names, listed in question 3.1? Please, provide examples. In OWL the preferred class name are probably captured using the rdfs:label idiom and foreign language translation via another rdfs:label idiom with the lang attribute set. Synonyms are probably captured by some self-created OWL annotation properties or in OBO by the 'exact_synonym' idiom. *3.3 *Do you think there is a need to expand the expressivity of the ontology representation languages in order to provide more naming flexibility? What elements are missing? *3.4* Did you use any features/functions of your ontology editor to check for consistency within the names? In Prot?g? these features would be the browser key, PROMPT or StringSearchTab, and the redundancy check functionality in OBO Edit. Specialized software tools also exist to check naming conventions, e.g. Validator (http://www.kismeta.com/Validtr.html) _4. In depth questions on specific naming conventions_ *4.1 Explicit and concise names and context independence* *4.1.1* Do you put any constraints on the use of natural language? For example, do you omit nouns, articles or other words to ensure shorter names, e.g. /'two dimensional J-resolved', /in place of /'the two dimensional J-resolved pulse sequence'? /If yes, please describe. *4.1.2* Do you make sure all the names are understandable on their own, even when viewed outside of the immediate context? *4.2 Compound names* *4.2.1* Do you apply any conventions that help string matching? For example, when creating compound names do you try to build the names out of already defined building blocks, re-using the same words or word-parts (affixes) present in other names and other representational units? For example, use 'x_part_of_process', 'y_part_of_process' and 'z_part_of_process' using consistently the string 'part of' (used and defined elsewhere) instead of using also a synonymous strings e.g. 'x_component_of_process', 'y_part_of_process', 'z_portion_of_process', introducing heterogeneity. GO for example re-uses the string 'development' in such a defined way all over in its class names. *4.2.2* Do your names contain defined strings that have a special defined meaning in each occurrence? Defined strings could indicate administrative metadata, e.g. as in the names '?device' or 'device refine'. GO used the 'sensu' string to constrain validity, e.g. species specificity as in 'fruiting body development (sensu Bacteria)' (GO:0030583, Note that the 'sensu' practice is now discouraged in GO in favour of stating appropriate differentia explicitly and avoiding the taxon in names and definitions, e.g. 'cell wall (sensu bacteria)' becomes 'peptidoglycan-based cell wall' ). *4.2.3 *Have you developed any guidelines to create compound names? For example conventions that demand a specific order of types of words within the name. *4.3 Homonyms* *4.3.1 *How do you cope with homonyms and highly ambiguous names? For example, one can try to avoid or disambiguate homonyms like 'set', which can indicate a plurality as in 'protocol set', as well as an action as in 'parameter set'. OpenCyc uses qualifiers as name suffixes to disambiguate homonyms, e.g. 'Plant-the factory' vs. 'Plant-the organism'. *4.4 Consistency of language* *4.4.1* Do you consistently apply British or US English word forms? For example using 'polymerising' vs. 'polymerizing' throughout. *4.4.2* Do you encounter cases where inconsistency arises from including words from different languages? If yes, please explain how you tackle these inconsistencies. For example, 'gut' is the English word for the Latin 'intestine' *4.5 Noun and verb forms* *4.5.1* Do you encode word forms consciously and in a consistent way within your names and do you have any guidelines regarding word forms? For example, using 'to be measured' (future) and 'measured' (past) or the time-neutral noun form 'measurement' in certain circumstances only. *4.6 Abbreviations and acronyms* *4.6.1 *How do you handle acronyms and abbreviations and how do you deal with widely used acronyms, .e.g. 'NMR' that would result in very long name when resolved? Could a /cut-off/ be defined when an acronym can be used in a name and still be intuitive and understandable throughout the domain? *4.7 Singularity* *4.7.1* Do you capture plural or singular word forms throughout your ontology? When capturing pluralities, do you use a consistent naming convention? For example one could restrict the usage of plurality indicators, e.g. either 'Xs' 'X collection', 'X set', or 'aggregate of X' throughout. *4.8 Positive names* *4.8.1 *Do you apply negative names such as 'non-separation device'? *4.8.2 *Do you explicitly exclude things within your names? For example in gene ontology one can find 'hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides ' (GO:0016812 ). *4.9 Conjunctions* *4.9.1* Do the names in your ontology contain logical connectives and Boolean operators such as 'or' or 'and', e.g. as in 'strain or line' or ' antigen processing and presentation of peptide or polysaccharide antigen via MHC class II ' (GO:0002504 )? *4.9.2* Do the names in your ontology contain hyphens, slashes, parenthesis or other symbols and if so, do you use them consistently? If yes, please explain their meaning and use. In many ontologies currently the hyphen and slashes are used with different underlying meanings. Hyphens can indicate omissions in names (ellipse or apocope), e.g. 'gene-technology' for 'gene modification technology', indicate logical connectives, e.g. 'black-white', or ranges, e.g. '10-100'. *4.10 Taboo words* *4.10.1* Do names in your ontology contain words that refer to the representational units (e.g. class or relation) they are encoded in, rather than to what is represented For example as in 'protocol class', 'animal type', 'color attribute', 'ligand relation'. *4.11 Typography* *4.11.1* Which typographical convention, e.g. lower case, UPPERCASE, mixed Case or CamelCase do you use for the categories of names (listed in question 3.1)? Under the OBO umbrella one can find 'MyClass' 'My Class', 'My-Class', 'My_Class', 'My_class' and 'my class' conventions, even within one ontology and throughout different representational idioms. In the AI community the convention to have classes starting upper-case and relations and instances starting lower-case is common. *4.11.2* Do you use sub- or superscripts or other text formatting to encode additional information? *4.11.3* Do you use any character as a word separator (such as '_', '-', ' ', etc. ) within compound names? If yes, please, explain the reason of your choice. For example, XML based languages, such as OWL, cannot have the space separator, because they need to be a valid when part of URIs, where space is not allowed. CamelCase is problematic for text mining since indicators for word-borders are lost in CamelCase. *4.11.4* How do you handle chemical element symbols, Greek symbols like *a**,** *and other special characters like *? C** *? *4.11.5* Do you have to handle product names or registered brand names? If yes, how do you render their names intuitive (or do you capture them as they are) ? A brand name 'US 2', describing an NMR magnet, could be renamed by using the company name as prefix, the product brand name as infix and the product type (superclass) as headword/suffix, e.g. use 'Bruker US 2 NMR magnet'. *Lastly, is there any final comment you want to make, including additional questions that should have been in this questionnaire? Has every naming issue you came across been covered?* *THANKS* -------------- next part -------------- An HTML attachment was scrubbed... URL: From cwt6 at cornell.edu Wed Jan 16 21:38:02 2008 From: cwt6 at cornell.edu (Chih-Wei Tung) Date: Wed, 16 Jan 2008 18:38:02 -0800 Subject: [Po-dev] The Plant Ontology Database in NAR 2008 DB issue Message-ID: <63542534-79DF-46A0-8599-CF80BA9B7D96@cornell.edu> Dear all, We are pleased to inform you that "The Plant Ontology Database" paper is appeared on NAR 2008 database issue now! Please visit the article on-line at http://nar.oxfordjournals.org/cgi/ content/full/36/suppl_1/D449 Thank you all for making significant intellectual contributions to the POC! Chih-Wei From rhee at acoma.stanford.edu Wed Jan 16 21:41:44 2008 From: rhee at acoma.stanford.edu (Sue Rhee) Date: Wed, 16 Jan 2008 18:41:44 -0800 Subject: [Po-dev] The Plant Ontology Database in NAR 2008 DB issue In-Reply-To: <63542534-79DF-46A0-8599-CF80BA9B7D96@cornell.edu> References: <63542534-79DF-46A0-8599-CF80BA9B7D96@cornell.edu> Message-ID: <478EC068.90005@acoma.stanford.edu> Wonderful. Congratulations, Sue Chih-Wei Tung wrote: > Dear all, > > We are pleased to inform you that "The Plant Ontology Database" paper > is appeared on NAR 2008 database issue now! > Please visit the article on-line at > http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D449 > > Thank you all for making significant intellectual contributions to the > POC! > > Chih-Wei > > > _______________________________________________ > Po-dev mailing list > Po-dev at plantontology.org > http://mail.plantontology.org/mailman/listinfo/po-dev -- Sue Rhee Staff Scientist Carnegie Institution, Department of Plant Biology 260 Panama Street, Stanford, CA 94305 Email: (650) 325-1521 x251 Fax: (650) 325-6857 From kellogge at umsl.edu Thu Jan 17 09:35:41 2008 From: kellogge at umsl.edu (Elizabeth Kellogg) Date: Thu, 17 Jan 2008 08:35:41 -0600 Subject: [Po-dev] The Plant Ontology Database in NAR 2008 DB issue In-Reply-To: <63542534-79DF-46A0-8599-CF80BA9B7D96@cornell.edu> Message-ID: Looks great - thanks! Toby On 1/16/08 8:38 PM, "Chih-Wei Tung" wrote: > content/full/36/suppl_1/D449 From cwt6 at cornell.edu Thu Jan 17 10:32:15 2008 From: cwt6 at cornell.edu (Chih-Wei Tung) Date: Thu, 17 Jan 2008 07:32:15 -0800 Subject: [Po-dev] Re: [Gramene-dev] Gramene Development Site Feedback: The "browse" link is not working In-Reply-To: References: <200801170032.m0H0WKth026412@gorgonzola.cshl.edu> <33DB9D1D-FBD0-4D33-8505-88671A3EEF25@cornell.edu> Message-ID: Hi Liya, In this page http://www.gramene.org/plant_ontology/ ontology_browse.html, there is "browse" link next to each different ontology, when I click the "browse", it directs me to the url "www2.gramene.org/db Chih-Wei On Jan 17, 2008, at 5:31 AM, Liya Ren wrote: > Hi Chih-Wei, > > Why you use 'www2' ?, the url is 'www' > > Liya > > On Jan 16, 2008, at 9:40 PM, Chih-Wei Tung wrote: > >> Hi Liya, >> >> Could you check it again? the "browse" links are still not >> working. For example, http://www2.gramene.org/db/ontology/search? >> id=GO:0005575 >> >> Chih-wei >> >> >> >> On Jan 16, 2008, at 5:20 PM, Liya Ren wrote: >> >>> Hi Chih-Wei, >>> >>> It is not only this page not working, the whole live site is >>> down. Now I have restarted the web server and it is working. >>> >>> Liya >>> >>> On Jan 16, 2008, at 7:32 PM, possible_feedback at acorn.gramene.org >>> wrote: >>> >>>> URL : http://www.gramene.org/plant_ontology/ >>>> ontology_browse.html >>>> >>>> Subject : Gramene Development Site Feedback: The "browse" >>>> link is not working >>>> >>>> Name : chih-wei >>>> >>>> Email : cwt6 at cornell.edu >>>> >>>> Organization: cu >>>> >>>> Comments : >>>> >>>> Hi, >>>> >>>> The "browse" link in this page are not working. Please check. >>>> Thank you. >>>> >>>> Chih-Wei >>>> >>>> >>>> Submitted by Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1; >>>> SV1; InfoPath.2) from 66.181.12.66 >>>> >>>> _______________________________________________ >>>> Gramene-dev mailing list >>>> Gramene-dev at gramene.org >>>> http://mail.gramene.org/mailman/listinfo/gramene-dev >>> >> > From schober at ebi.ac.uk Tue Jan 29 14:07:56 2008 From: schober at ebi.ac.uk (Daniel Schober) Date: Tue, 29 Jan 2008 19:07:56 +0000 Subject: [Po-dev] Reminder - Shaping OBO Foundry naming conventions - survey: input sollicited In-Reply-To: <4786114B.2030706@ebi.ac.uk> References: <4786114B.2030706@ebi.ac.uk> Message-ID: <479F798C.4030601@ebi.ac.uk> Dear Plant Ontology curators. /[ This email is being sent at the request of the OBO Foundry coordinators Barry Smith, Suzi Lewis, Chris Mungall and Michael Ashburner]/ I am approaching you regarding your role as an editor/curator of the following ontologies: *Plant growth and developmental stage , http://www.obofoundry.org/cgi-bin/detail.cgi?id=po_temporal Plant structure , http://www.obofoundry.org/cgi-bin/detail.cgi?id=po_anatomy* This is an opportunity for you and your ontology community to *help OBO Foundry** shape **guidelines for naming conventions*. I would appreciate *your input to our survey* on your current practice in naming (labeling) entities within your ontology. The questionnaire is copied below and it is also available at the OBO Foundry wiki http://obofoundry.org/wiki/index.php/Naming Please, fill out the attached *questionnaire *and send it back to me, or alternatively let me know if you are available for a *phone *or *skype interview *and your contact details. The first phase of the survey has been completed and we have already collected answers from* 34 *ontologies! This second and last part of the survey will be closed by Feb 8th and results posted at the OBO Foundry wiki page. If you have any question, please don't hesitate to contact me. Thanks in advance for your reply! Best regards, Daniel Schober * *** The OBO Foundry paper is out in Nature Biotechnology http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf ***** _naming conventions - SURVEY_ Scope The overall goals of this survey are twofold: 1. to evaluate the current practice in naming entities within the OBO ontology working groups 2. to move towards a common set of naming convention for the OBO Foundy Further details on the rationale for this survey can be found in Schober /et al/. 2007, "Towards naming conventions for use in controlled vocabulary and ontology engineering", _http://bio-ontologies.org.uk/download/Bio-Ontologies2007.pdf_, pages 29-32. Results Any questions as well as the completed questionnaires should be sent to Daniel Schober (schober at ebi.ac.uk). The outcome will be posted on the OBO Foundry wiki pages (http://obofoundry.org/wiki/index.php/Naming) and all participants will get notified accordingly. // Questionnaire _1. Questions on your ontology and its engineering and maintenance process_ *1.1 *Are you and your co-workers familiar with the OBO Foundry principles (http://www.obofoundry.org/crit.shtml)? *1.2* If yours in an OBO Foundry ontology, have you started implementing these principles and aligned your development process accordingly? *1.3* Is work on your ontology closely associated with the need to manage and formulate queries about a specific body of data? If so, can you specify the type of data? This question refers to the instance level and annotated data bodies. Is the ontology developed in collaboration with the maintenance of a database or collection of databases (as the GO is developed in collaboration with UniProt and with various MOD databases)? *1.4* Which ontology editor tool(s) do you use to build and manage your ontology? *1.5 *Please illustrate the editing process, i.e. is your ontology developed in a centralised or distributed manner? In both cases, please, state the number of people directly handling and editing the ontology file and if they are physically distributed or if they are located in one spot. *1.6* Do you introduce special /helper classes/ or /bins/, that refer to metadata to facilitate the engineering process? If yes, please describe them and explain how do you indicate their special status? Examples are 'obsolete classes', 'imported classes', 'deleted classes'. _2. General questions on your current practice in naming entities and their documentation_ *2.1* Have you developed naming conventions within your ontology community? If yes, please specify how these are formulated, e.g. as a specific, standalone document or as part of other documentation and where these are available, e.g. provide URL. *2.2 *(If your answer to 2.1 is positive) Which entities are tackled by your naming conventions? Some examples are provided below, add if required: * class names * relation names, e.g. colour vs has_colour vs colour_of * instance names * the name of the ontology, its versions, namespaces and term IDs *2.3* (If your answer to 2.1 is negative) Have you re-used existing naming conventions from other ontology groups? For example have you applied the GO editor style guide or conventions from other sources, e.g. ontology tutorials or guidelines from standardization bodies such as ISO? _3. Questions on the implementation of names_ *3.1 *Which of the following categories of names (or name types) do you record in your ontology and which one do you anticipate such common naming conventions are useful for?// Some examples are provided below, add if required:// ? preferred name ? short name or display name ? formal name ? synonym ? foreign language translations ? broader or narrower term *3.2* (If applicable) Which ontology language idioms do you use to capture the categories of names, listed in question 3.1? Please, provide examples. In OWL the preferred class name are probably captured using the rdfs:label idiom and foreign language translation via another rdfs:label idiom with the lang attribute set. Synonyms are probably captured by some self-created OWL annotation properties or in OBO by the 'exact_synonym' idiom. *3.3 *Do you think there is a need to expand the expressivity of the ontology representation languages in order to provide more naming flexibility? What elements are missing? *3.4* Did you use any features/functions of your ontology editor to check for consistency within the names? In Prot?g? these features would be the browser key, PROMPT or StringSearchTab, and the redundancy check functionality in OBO Edit. Specialized software tools also exist to check naming conventions, e.g. Validator (http://www.kismeta.com/Validtr.html) _4. In depth questions on specific naming conventions_ *4.1 Explicit and concise names and context independence* *4.1.1* Do you put any constraints on the use of natural language? For example, do you omit nouns, articles or other words to ensure shorter names, e.g. /'two dimensional J-resolved', /in place of /'the two dimensional J-resolved pulse sequence'? /If yes, please describe. *4.1.2* Do you make sure all the names are understandable on their own, even when viewed outside of the immediate context? *4.2 Compound names* *4.2.1* Do you apply any conventions that help string matching? For example, when creating compound names do you try to build the names out of already defined building blocks, re-using the same words or word-parts (affixes) present in other names and other representational units? For example, use 'x_part_of_process', 'y_part_of_process' and 'z_part_of_process' using consistently the string 'part of' (used and defined elsewhere) instead of using also a synonymous strings e.g. 'x_component_of_process', 'y_part_of_process', 'z_portion_of_process', introducing heterogeneity. GO for example re-uses the string 'development' in such a defined way all over in its class names. *4.2.2* Do your names contain defined strings that have a special defined meaning in each occurrence? Defined strings could indicate administrative metadata, e.g. as in the names '?device' or 'device refine'. GO used the 'sensu' string to constrain validity, e.g. species specificity as in 'fruiting body development (sensu Bacteria)' (GO:0030583, Note that the 'sensu' practice is now discouraged in GO in favour of stating appropriate differentia explicitly and avoiding the taxon in names and definitions, e.g. 'cell wall (sensu bacteria)' becomes 'peptidoglycan-based cell wall' ). *4.2.3 *Have you developed any guidelines to create compound names? For example conventions that demand a specific order of types of words within the name. *4.3 Homonyms* *4.3.1 *How do you cope with homonyms and highly ambiguous names? For example, one can try to avoid or disambiguate homonyms like 'set', which can indicate a plurality as in 'protocol set', as well as an action as in 'parameter set'. OpenCyc uses qualifiers as name suffixes to disambiguate homonyms, e.g. 'Plant-the factory' vs. 'Plant-the organism'. *4.4 Consistency of language* *4.4.1* Do you consistently apply British or US English word forms? For example using 'polymerising' vs. 'polymerizing' throughout. *4.4.2* Do you encounter cases where inconsistency arises from including words from different languages? If yes, please explain how you tackle these inconsistencies. For example, 'gut' is the English word for the Latin 'intestine' *4.5 Noun and verb forms* *4.5.1* Do you encode word forms consciously and in a consistent way within your names and do you have any guidelines regarding word forms? For example, using 'to be measured' (future) and 'measured' (past) or the time-neutral noun form 'measurement' in certain circumstances only. *4.6 Abbreviations and acronyms* *4.6.1 *How do you handle acronyms and abbreviations and how do you deal with widely used acronyms, .e.g. 'NMR' that would result in very long name when resolved? Could a /cut-off/ be defined when an acronym can be used in a name and still be intuitive and understandable throughout the domain? *4.7 Singularity* *4.7.1* Do you capture plural or singular word forms throughout your ontology? When capturing pluralities, do you use a consistent naming convention? For example one could restrict the usage of plurality indicators, e.g. either 'Xs' 'X collection', 'X set', or 'aggregate of X' throughout. *4.8 Positive names* *4.8.1 *Do you apply negative names such as 'non-separation device'? *4.8.2 *Do you explicitly exclude things within your names? For example in gene ontology one can find 'hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides ' (GO:0016812 ). *4.9 Conjunctions* *4.9.1* Do the names in your ontology contain logical connectives and Boolean operators such as 'or' or 'and', e.g. as in 'strain or line' or ' antigen processing and presentation of peptide or polysaccharide antigen via MHC class II ' (GO:0002504 )? *4.9.2* Do the names in your ontology contain hyphens, slashes, parenthesis or other symbols and if so, do you use them consistently? If yes, please explain their meaning and use. In many ontologies currently the hyphen and slashes are used with different underlying meanings. Hyphens can indicate omissions in names (ellipse or apocope), e.g. 'gene-technology' for 'gene modification technology', indicate logical connectives, e.g. 'black-white', or ranges, e.g. '10-100'. *4.10 Taboo words* *4.10.1* Do names in your ontology contain words that refer to the representational units (e.g. class or relation) they are encoded in, rather than to what is represented For example as in 'protocol class', 'animal type', 'color attribute', 'ligand relation'. *4.11 Typography* *4.11.1* Which typographical convention, e.g. lower case, UPPERCASE, mixed Case or CamelCase do you use for the categories of names (listed in question 3.1)? Under the OBO umbrella one can find 'MyClass' 'My Class', 'My-Class', 'My_Class', 'My_class' and 'my class' conventions, even within one ontology and throughout different representational idioms. In the AI community the convention to have classes starting upper-case and relations and instances starting lower-case is common. *4.11.2* Do you use sub- or superscripts or other text formatting to encode additional information? *4.11.3* Do you use any character as a word separator (such as '_', '-', ' ', etc. ) within compound names? If yes, please, explain the reason of your choice. For example, XML based languages, such as OWL, cannot have the space separator, because they need to be a valid when part of URIs, where space is not allowed. CamelCase is problematic for text mining since indicators for word-borders are lost in CamelCase. *4.11.4* How do you handle chemical element symbols, Greek symbols like *a**,** *and other special characters like *? C** *? *4.11.5* Do you have to handle product names or registered brand names? If yes, how do you render their names intuitive (or do you capture them as they are) ? A brand name 'US 2', describing an NMR magnet, could be renamed by using the company name as prefix, the product brand name as infix and the product type (superclass) as headword/suffix, e.g. use 'Bruker US 2 NMR magnet'. *Lastly, is there any final comment you want to make, including additional questions that should have been in this questionnaire? Has every naming issue you came across been covered?* *THANKS* -------------- next part -------------- An HTML attachment was scrubbed... URL: