From cwt6 at cornell.edu Thu Aug 23 15:20:35 2007 From: cwt6 at cornell.edu (Chih-Wei Tung) Date: Thu, 23 Aug 2007 15:20:35 -0400 Subject: [Po-dev] Fruit cortex and fruit core Message-ID: <4D9B56F5-FF50-4503-84EA-A207AB1AF1FC@cornell.edu> Hi, Rosaceae community, I have a question regarding to the fruit structure terminology which are used in GDR database "genebank apple cDNA library" (http:// www.bioinfo.wsu.edu/gdr/projects/malus/unigeneV3/ malus_librarySummary.shtml). Please help me to define or clarify the following terms, I will add them either as new ontology terms or synonyms to the existing plant ontology based on your answers fruit cortex -> is it the same as flesh or mesocarp? are these three terms used interchangeable? fruit core -> is this the tissue in the center of the fruit as seen in http://www.uq.edu.au/_School_Science_Lessons/5.6FruitPome.GIF? does it include seeds? what's the definition? Currently Plant Ontology database has "fruit placenta: a more or less localized region within a fruit to which seeds are attached", can "fruit placenta" be a synonym to "fruit core"? Your opinion and comments are sincerely appreciated! Thank you, Chih-Wei Tung Plant Ontology Consortium Cornell University Ithaca, NY www.plantontology.org From cwt6 at cornell.edu Thu Aug 23 22:07:33 2007 From: cwt6 at cornell.edu (Chih-Wei Tung) Date: Thu, 23 Aug 2007 22:07:33 -0400 Subject: [Po-dev] Fruit cortex and fruit core In-Reply-To: References: <4D9B56F5-FF50-4503-84EA-A207AB1AF1FC@cornell.edu> Message-ID: Hi Peter, Thank you for the quick answer. You mentioned Potter et al use Spjut's fruit terms in Rosaceae, do you have that reference? I found one article " A systematic Treatment of Fruit Types " by Richard Spjut from http://www.worldbotanical.com/fruit_types.htm, is this the guide we can follow? I will check our library to see if they have Spjut's book too. Thank you again, Chih-Wei On 8/23/07, Peter Stevens wrote: > > Oh dear, we venture into the swamp of rosaceous fruit terms! If we > are thinking of Rosaceae, the core of an apple is basically a fruit > proper, i.e. the post fertilisation products of the gynoecium. The > cortex is probably hypanthial tissue, mesocarp refers to tissues of a > true fruit, i.e., it has little to do with what we eat in an apple > (but a great deal t do wit what we relish in raspberries or > blackberries (which of course are not berries) and flesh can refer to > anything fleshy irrespective of actual origin, including the flesh of > a strawberry, which also is not a berry, but neither is it a "pome" - > the fruit of an apple, rather, it has a lot of achenes distributed > over the surface of an enlarged and fleshy receptacle. So the three > terms that you mention are not interchangeable, and the third > (flesh) should not be usedin an ontology. The 'fruit skin peel' of > the GDR database has nothing to do with the fruit s. str., but is the > epidermis and maybe a few adjacent cells of the hypanthium. > > Note that in a recent paper Potter et al. use Spjut's fruit terms for > fruits of Rosaceae, for which you will need Spjut as a guide... > > I hope this helps. > > P. > On Aug 23, 2007, at 2:20 PM, Chih-Wei Tung wrote: > > > Hi, Rosaceae community, > > > > I have a question regarding to the fruit structure terminology > > which are used in GDR database "genebank apple cDNA > > library" (http://www.bioinfo.wsu.edu/gdr/projects/malus/unigeneV3/ > > malus_librarySummary.shtml). > > Please help me to define or clarify the following terms, I will add > > them either as new ontology terms or synonyms to the existing plant > > ontology based on your answers > > > > fruit cortex -> is it the same as flesh or mesocarp? are these > > three terms used interchangeable? > > fruit core -> is this the tissue in the center of the fruit as seen > > in http://www.uq.edu.au/_School_Science_Lessons/5.6FruitPome.GIF? > > does it include seeds? what's the definition? > > Currently Plant Ontology database has "fruit placenta: a more or > > less localized region within a fruit to which seeds are attached", > > can "fruit placenta" be a synonym to "fruit core"? > > > > Your opinion and comments are sincerely appreciated! > > > > Thank you, > > > > Chih-Wei Tung > > Plant Ontology Consortium > > Cornell University > > Ithaca, NY > > www.plantontology.org > > _______________________________________________ > > Po-dev mailing list > > Po-dev at plantontology.org > > http://mail.plantontology.org/mailman/listinfo/po-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cwt6 at cornell.edu Fri Aug 24 11:48:38 2007 From: cwt6 at cornell.edu (Chih-Wei Tung) Date: Fri, 24 Aug 2007 11:48:38 -0400 Subject: [Po-dev] Fruit cortex and fruit core In-Reply-To: References: <4D9B56F5-FF50-4503-84EA-A207AB1AF1FC@cornell.edu> Message-ID: <8C853133-077D-4933-A39D-9906587749D1@cornell.edu> Peter, No problem, I will keep your advise in mind, and thank you for sharing the information. Chih-Wei On Aug 24, 2007, at 10:08 AM, Peter Stevens wrote: > Please, do not introduce these fruit terms further into the > literature! Botany in burdened enough with such terms. I find it > far better simply to describe the morphology of fruits (some terms > such as berry, achene, etc., are fine). Thus people have used > anthocarp for things like morning glory fruits, but then > Dipterocarpaceae have anthocarps although they might be > pseudosamara acc. to Spjut (but then again, they might not). And > blueberries are close to apples in morphology, so if apples are > pomes, then blueberries may be, too... And Spjut's work, although > comprehensive, will need still further elaboration; maybe in the > book Stuppy and he are writing. I will have to ait in patience. > There is a reference to Potter et al. 2007 on /APweb/. > > > On Aug 23, 2007, at 9:07 PM, Chih-Wei Tung wrote: > >> Hi Peter, >> >> Thank you for the quick answer. You mentioned Potter et al use >> Spjut's fruit terms in Rosaceae, do you have that reference? I >> found one article " A systematic Treatment of Fruit Types " by >> Richard Spjut from http://www.worldbotanical.com/fruit_types.htm, >> is this the guide we can follow? I will check our library to see >> if they have Spjut's book too. >> >> Thank you again, >> >> Chih-Wei >> >> >> >> On 8/23/07, Peter Stevens wrote: >> Oh dear, we venture into the swamp of rosaceous fruit terms! If we >> are thinking of Rosaceae, the core of an apple is basically a fruit >> proper, i.e. the post fertilisation products of the gynoecium. The >> cortex is probably hypanthial tissue, mesocarp refers to tissues of a >> true fruit, i.e., it has little to do with what we eat in an apple >> (but a great deal t do wit what we relish in raspberries or >> blackberries (which of course are not berries) and flesh can refer to >> anything fleshy irrespective of actual origin, including the flesh of >> a strawberry, which also is not a berry, but neither is it a "pome" - >> the fruit of an apple, rather, it has a lot of achenes distributed >> over the surface of an enlarged and fleshy receptacle. So the three >> terms that you mention are not interchangeable, and the third >> (flesh) should not be usedin an ontology. The 'fruit skin peel' of >> the GDR database has nothing to do with the fruit s. str., but is the >> epidermis and maybe a few adjacent cells of the hypanthium. >> >> Note that in a recent paper Potter et al. use Spjut's fruit terms for >> fruits of Rosaceae, for which you will need Spjut as a guide... >> >> I hope this helps. >> >> P. >> On Aug 23, 2007, at 2:20 PM, Chih-Wei Tung wrote: >> >> > Hi, Rosaceae community, >> > >> > I have a question regarding to the fruit structure terminology >> > which are used in GDR database "genebank apple cDNA >> > library" (http://www.bioinfo.wsu.edu/gdr/projects/malus/unigeneV3/ >> > malus_librarySummary.shtml). >> > Please help me to define or clarify the following terms, I will add >> > them either as new ontology terms or synonyms to the existing plant >> > ontology based on your answers >> > >> > fruit cortex -> is it the same as flesh or mesocarp? are these >> > three terms used interchangeable? >> > fruit core -> is this the tissue in the center of the fruit as seen >> > in http://www.uq.edu.au/_School_Science_Lessons/5.6FruitPome.GIF ? >> > does it include seeds? what's the definition? >> > Currently Plant Ontology database has "fruit placenta: a more or >> > less localized region within a fruit to which seeds are attached", >> > can "fruit placenta" be a synonym to "fruit core"? >> > >> > Your opinion and comments are sincerely appreciated! >> > >> > Thank you, >> > >> > Chih-Wei Tung >> > Plant Ontology Consortium >> > Cornell University >> > Ithaca, NY >> > www.plantontology.org >> > _______________________________________________ >> > Po-dev mailing list >> > Po-dev at plantontology.org >> > http://mail.plantontology.org/mailman/listinfo/po-dev >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From schober at ebi.ac.uk Fri Aug 31 06:58:33 2007 From: schober at ebi.ac.uk (Daniel Schober) Date: Fri, 31 Aug 2007 11:58:33 +0100 Subject: [Po-dev] Reminder: OBO Foundry naming conventions survey - input required Message-ID: <46D7F459.5020804@ebi.ac.uk> /This is a reminder to our previous email, see below. Please try to respond before 4th of September. Filling out the questionnaire will take under an hour./ 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 as an editors of the plant growth and development stage ontology and would appreciate your input to our survey on your current practice in naming (labeling) entities within your ontology or controlled vocabulary. The questionnaire is copied below and it is also available at the OBO Foundry wiki http://obofoundry.org/wiki/index.php/Naming Please, fill it out and send it back to me, or alternatively let me know if an ontology editor is available for a phone or skype interview. Thanks in advance for your reply! Best regards, Daniel Schober _ PS: _Note that the survey will be closed by September 7th and result posted at the wiki page. If you have any question, please don't hesitate to contact me (schober at ebi.ac.uk). --- _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* -- __________________________________________________________________________________________ Dr. Daniel Schober NET Project - Ontologist The European Bioinformatics Institute email: schober at ebi.ac.uk EMBL Outstation - Hinxton direct: +44 (0)1223 494410 Wellcome Trust Genome Campus fax: +44 (0)1223 494 468 Cambridge CB10 1SD, UK Room: A3-141 (extension building) Project page: www.ebi.ac.uk/net-project Personal page: http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734 Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/ -------------- next part -------------- An HTML attachment was scrubbed... URL: