From gordonp at cbr.nrc.ca Tue Jul 6 11:58:44 2004 From: gordonp at cbr.nrc.ca (Paul Gordon) Date: Tue Jul 6 12:00:53 2004 Subject: [MOBY-l] The fun begins Message-ID: <40EACC34.2060007@cbr.nrc.ca> Hi all, I am reworking the MobyRequest class to work with Apache Axis 1.1beta, since 1.0 has a very crappy ClassLoader that is slowing down my applets by generating 100's of needless HTTP requests. While doing this, I'm trying to make sure I parse SOAP messages as generically as possible. The following is the first of several quirks I'm finding in almost all services: The SOAP response is getting the namespace http://biomoby.org/ rather than http://www.biomoby.org/moby as specified in the API for all the rest of the markup. Is the envelope node (or nodes since sometimes the xxxResponse is wrapped in a xxxReturn) meant to be in a separate namespace from the contents? If so, shouldn't we call it something like http://biomoby.org/transport for clarity's sake? From barbara.re at studenti.unicam.it Tue Jul 6 13:39:12 2004 From: barbara.re at studenti.unicam.it (RE BARBARA) Date: Tue Jul 6 13:41:20 2004 Subject: [MOBY-l] request about getNamespace() in MobyData Message-ID: <1089135552.40eae3c0aa2a3@mail.studenti.unicam.it> Hi, once extract the input of a service (through the Bees java), as can I do for extracting, for examples, the Data Type or Namespaces? I don't succeed in using the method "getNamespaces()" or "getDataType()" because the method getPrimaryInputs() returns me a type MobyData while the methods "getNamespaces()" or "getDataType()" require MobyPrimaryDataSimple. How can I do? Barbara From senger at ebi.ac.uk Tue Jul 6 20:42:14 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Tue Jul 6 20:44:26 2004 Subject: [MOBY-l] request about getNamespace() in MobyData In-Reply-To: <1089135552.40eae3c0aa2a3@mail.studenti.unicam.it> References: <1089135552.40eae3c0aa2a3@mail.studenti.unicam.it> Message-ID: <23733.202.123.48.250.1089160934.squirrel@webmail.ebi.ac.uk> Hi, Please forgive me if I has not understood correctly your question, but if I have then here is an answer: > I don't succeed in using the method "getNamespaces()" or "getDataType()" > because the method getPrimaryInputs() returns me a type MobyData while the > methods "getNamespaces()" or "getDataType()" require > MobyPrimaryDataSimple. > MobyPrimaryDataSimple inherits from MobyData. So, actually,the method getPrimaryInputs() only seems to return MobyData but in fact it returns more specific type, e.g. MobyPrimaryDataSimple. So, just cast it. Regards, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From mwilkinson at mrl.ubc.ca Mon Jul 12 02:35:43 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Mon Jul 12 01:37:51 2004 Subject: [MOBY-l] Cleaning up the MOBY Central registry Message-ID: <1089614143.1823.35.camel@myhost.mydomain> Hi all, I want to clean up the registry now that there is a separate test registry up and running. The following services seem to be "litter" (folks at IRRI - can you confirm/deny this for your services?). unless I hear otherwise I will delete them from the registry in the next few days. +--------------------------+----------------------+ | servicename | authority_uri | +--------------------------+----------------------+ | test3_SequenceToFASTA | ccgb.umn.edu | | test_getgermplasm | www.iris.irri.org | | test_getgermplasm_wtrait | www.iris.irri.org | | test_getstudy | www.iris.irri.org | | test_gettrait | www.iris.irri.org | | test_SequenceToFASTA | ccgb.umn.edu | | test_SequenceToFASTA | cilantro.bio.unc.edu | | test_u26230 | mobyed1.sdsc.edu | +--------------------------+----------------------+ Cheers! M -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From mwilkinson at mrl.ubc.ca Mon Jul 12 02:37:56 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Mon Jul 12 01:40:01 2004 Subject: [MOBY-l] cleaning up the ontologies Message-ID: <1089614276.1823.37.camel@myhost.mydomain> Hi again, The same goes for these objects (yeah, I see some of my own are in there as well...) +----------------------------------+-------------------+---------------------+ | object_type | authority | contact_email | +----------------------------------+-------------------+---------------------+ | TEST | www.sdsc.edu | steube@sdsc.edu | | testString | www.illuminae.com | markw@illuminae.com | | test2String | www.illuminae.com | markw@illuminae.com | | MyTestingDataType_10809965326221 | testing.org | mail@mail.com | | testout | www.iris.irri.org | mulat@cgiar.org | +----------------------------------+-------------------+---------------------+ Unless I hear otherwise I will delete these in the next few days. M -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From bmg at sfu.ca Thu Jul 22 16:46:54 2004 From: bmg at sfu.ca (Benjamin Good) Date: Wed Jul 21 08:49:07 2004 Subject: [MOBY-l] An Ontology question Message-ID: <410027BE.7050303@sfu.ca> Hello Moby, It seems that the moby system would benefit from a semantically richer object ontology. Has anyone thought about ways to leverage existing ontologies (such as GO) for this purpose? curious to hear your thoughts -Ben From p.lord at russet.org.uk Wed Jul 21 10:28:10 2004 From: p.lord at russet.org.uk (Phillip Lord) Date: Wed Jul 21 10:33:20 2004 Subject: [MOBY-l] An Ontology question In-Reply-To: <410027BE.7050303@sfu.ca> References: <410027BE.7050303@sfu.ca> Message-ID: >>>>> "Benjamin" == Benjamin Good writes: Benjamin> Hello Moby, Benjamin> It seems that the moby system would benefit from a Benjamin> semantically richer object ontology. Has anyone thought Benjamin> about ways to leverage existing ontologies (such as GO) Benjamin> for this purpose? Benjamin> curious to hear your thoughts Well, GO itself describes the wrong thing, I think. MOBY needs an ontology of datatypes, and analyses. Several groups are thinking about producing semantically richer ontologies. Within the mygrid project (www.mygrid.org.uk) we have a fairly rich ontology (although possibly it's too rich!). Steffen Moeller has also developed a small service ontology, and the moby ontology is being worked on. I'm hoping that we can all get together on this and work together to generate a service ontology with good coverage, good usability, and clear semantics. Lots of scope for pub/restaurant discussions at ISMB, for those who are going to be there. If there is interest outside the people that I've already mentioned, then we should organise a small meeting (or "BOF" as people will insist on calling them). Cheers Phil From fgibbons at hms.harvard.edu Wed Jul 21 11:05:04 2004 From: fgibbons at hms.harvard.edu (Frank Gibbons) Date: Wed Jul 21 11:05:40 2004 Subject: [MOBY-l] An Ontology question In-Reply-To: <410027BE.7050303@sfu.ca> Message-ID: <5.2.1.1.2.20040721105107.01a031c8@email.med.harvard.edu> Hi Ben, I've been thinking about ways to extend the object (and service) ontology. In fact, as part of the BioGraphNet project for exchanging protein/genetic interaction networks (http://biographnet.sourceforge.net), Gabriel Berriz and I have added an 'interaction_partner' object, and then extended it with terms from the Proteomics Standards Initiative - Molecular Interaction (PSI-MI) controlled vocabulary for interaction_detection, at least to the first two levels. Since this is development work so far, most of these changes have been made in the test Registry that Mark put up a few weeks ago, not in the 'real' registry. So far, we've done this by hand, but clearly it would make much more sense to either automate it, or better yet, find a way to link from MOBY's object registry to a URI of PSI-MI's. Unfortunately, being an RDF newbie, I'm not really sure of the best way to do this, or even if it's possible. I know that Mark W. is meeting with the myGRID folks this summer, to discuss ways to re-use their massive ontology, so that may obviate any other plans. It strikes me that it might not be desirable to include any ontology in all of its gory detail, at least in the absence of appropriate tools to navigate and visualise MOBY's ontologies. Martin Senger has written some really useful tools for that, but they generate static images rather than interactive ones, so once below the spatial resolution of your printer/screen, it's not possible to read it, and it's close to that right now. Just a brain dump. What are you thinking? -Frank At 04:46 PM 7/22/2004, Benjamin Good wrote: >Hello Moby, > >It seems that the moby system would benefit from a semantically richer >object ontology. Has anyone thought about ways to leverage existing >ontologies (such as GO) for this purpose? > >curious to hear your thoughts >-Ben > > > >_______________________________________________ >moby-l mailing list >moby-l@biomoby.org >http://biomoby.org/mailman/listinfo/moby-l PhD, Computational Biologist, Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA. Tel: 617-432-3555 Fax: 617-432-3557 http://llama.med.harvard.edu/~fgibbons From p.lord at russet.org.uk Wed Jul 21 11:42:58 2004 From: p.lord at russet.org.uk (Phillip Lord) Date: Wed Jul 21 11:48:22 2004 Subject: [MOBY-l] An Ontology question In-Reply-To: <5.2.1.1.2.20040721105107.01a031c8@email.med.harvard.edu> References: <5.2.1.1.2.20040721105107.01a031c8@email.med.harvard.edu> Message-ID: >>>>> "Frank" == Frank Gibbons writes: Frank> So far, we've done this by hand, but clearly it would make Frank> much more sense to either automate it, or better yet, find a Frank> way to link from MOBY's object registry to a URI of Frank> PSI-MI's. Unfortunately, being an RDF newbie, I'm not really Frank> sure of the best way to do this, or even if it's possible. I Frank> know that Mark W. is meeting with the myGRID folks this Frank> summer, to discuss ways to re-use their massive ontology, so Frank> that may obviate any other plans. Frank> It strikes me that it might not be desirable to include any Frank> ontology in all of its gory detail, at least in the absence Frank> of appropriate tools to navigate and visualise MOBY's Frank> ontologies. Martin Senger has written some really useful Frank> tools for that, but they generate static images rather than Frank> interactive ones, so once below the spatial resolution of Frank> your printer/screen, it's not possible to read it, and it's Frank> close to that right now. One of the issues with any complex ontology is how to visualise it, and how to present it to the different kinds of user who might want to use it. Within GO, for example, the annotators, GO curators and end users all seem the same ontology. But its doesn't necessarily need to be this way. (Indeed GO slims are an acknowledgement of this). I think that mygrid ontology is too complex to present to the end user, per se, but having a layer which removes most of the complexity for display, well still leaving this complexity so that the underlying machinery can use it seems like a good approach. Personally I would like to realise the mygrid ontology in a number of inter-related forms; the idea would be to have an underlying OWL-DL based ontology (so that we can use reasoner support, which helps in the building of the ontology). Then we use this to generate representationally simpler ontologies. So a stripped down OBO style ontology (modelled as a DAG). Moby-s would probably need something half way in between--it needs data type information (sequence has-a string) in the ontology which would probably be out of place in a OBO ontology. So you'd have to add something back in. All of which makes development of the ontology somewhat more complex, but will, hopefully, make it easier for the end user. Which is probably the way that it should be. I managed to talk with Steffen about this earlier in the month, and should get a chance to talk with Mark at ISMB. I guess we should try and advertise a meeting as a BOF, as it looks like others might be interested. Incidentally, for those of you going to ISMB, who are interested in ontologies, I have to say, in an entirely unbiased manner, that the bio-ontologies SIG (http://bio-ontologies.man.ac.uk/) looks wonderful. Everyone should attend! Cheers Phil From lstein at cshl.edu Thu Jul 22 18:16:51 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Thu Jul 22 18:20:33 2004 Subject: [MOBY-l] My fortune for the day Message-ID: <200407221816.51892.lstein@cshl.edu> Hi Folks, My /usr/bin/fortune program popped up the following gem this evening: Oh Lord, won't you buy me a 4BSD? My friends all got sources, so why can't I see? Come all you moby hackers, come sing it out with me: To hell with the lawyers from AT&T! Amazing. Lincoln -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From edoneel at sdf.lonestar.org Fri Jul 23 05:52:47 2004 From: edoneel at sdf.lonestar.org (Bruce O'Neel) Date: Fri Jul 23 05:54:29 2004 Subject: [MOBY-l] My fortune for the day In-Reply-To: <200407221816.51892.lstein@cshl.edu> References: <200407221816.51892.lstein@cshl.edu> Message-ID: <20040723095247.GB12415@SDF.LONESTAR.ORG> For those of you who might not know: http://www.clueless.com/jargon3.0.0/moby.html A title of address (never of third-person reference), usually used to show admiration, respect, and/or friendliness to a competent hacker. "Greetings, moby Dave. How's that address-book thing for the Mac going?" On Thu, Jul 22, 2004 at 06:16:51PM -0400, Lincoln Stein wrote: > Hi Folks, > > My /usr/bin/fortune program popped up the following gem this evening: > > Oh Lord, won't you buy me a 4BSD? > My friends all got sources, so why can't I see? > Come all you moby hackers, come sing it out with me: > To hell with the lawyers from AT&T! > > Amazing. > > Lincoln > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- edoneel@sdf.lonestar.org SDF Public Access UNIX System - http://sdf.lonestar.org From p.lord at russet.org.uk Fri Jul 23 06:33:14 2004 From: p.lord at russet.org.uk (Phillip Lord) Date: Fri Jul 23 06:36:45 2004 Subject: [MOBY-l] My fortune for the day In-Reply-To: <200407221816.51892.lstein@cshl.edu> References: <200407221816.51892.lstein@cshl.edu> Message-ID: >>>>> "Lincoln" == Lincoln Stein writes: Lincoln> Hi Folks, Lincoln> My /usr/bin/fortune program popped up the following gem Lincoln> this evening: Lincoln> Oh Lord, won't you buy me a 4BSD? My friends all got Lincoln> sources, so why can't I see? Come all you moby Lincoln> hackers, come sing it out with me: To hell with the Lincoln> lawyers from AT&T! Lincoln> Amazing. If only Janis were still here to sing it..... Cheers Phil From lstein at cshl.edu Fri Jul 23 10:44:37 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Fri Jul 23 10:46:40 2004 Subject: [MOBY-l] My fortune for the day In-Reply-To: <20040723095247.GB12415@SDF.LONESTAR.ORG> References: <200407221816.51892.lstein@cshl.edu> <20040723095247.GB12415@SDF.LONESTAR.ORG> Message-ID: <200407231044.37043.lstein@cshl.edu> Bruce, thanks for the jargon pointer. I never knew that. I'm particularly intrigued about the old-style moby factor. By that definition, my current desktop machine has 116 micro-mobies. Lincoln On Friday 23 July 2004 05:52 am, Bruce O'Neel wrote: > For those of you who might not know: > > http://www.clueless.com/jargon3.0.0/moby.html > > A title of address (never of third-person reference), usually used to > show admiration, respect, and/or friendliness to a competent > hacker. "Greetings, moby Dave. How's that address-book thing for the > Mac going?" > > On Thu, Jul 22, 2004 at 06:16:51PM -0400, Lincoln Stein wrote: > > Hi Folks, > > > > My /usr/bin/fortune program popped up the following gem this evening: > > > > Oh Lord, won't you buy me a 4BSD? > > My friends all got sources, so why can't I see? > > Come all you moby hackers, come sing it out with me: > > To hell with the lawyers from AT&T! > > > > Amazing. > > > > Lincoln > > > > -- > > Lincoln D. Stein > > Cold Spring Harbor Laboratory > > 1 Bungtown Road > > Cold Spring Harbor, NY 11724 > > _______________________________________________ > > moby-l mailing list > > moby-l@biomoby.org > > http://biomoby.org/mailman/listinfo/moby-l -- Lincoln Stein lstein@cshl.edu Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) From VNarayan at mail.brc.mcw.edu Fri Jul 23 17:25:20 2004 From: VNarayan at mail.brc.mcw.edu (Vijay Narayanasamy) Date: Fri Jul 23 17:32:29 2004 Subject: [MOBY-l] BioMOBY Service Failure Message-ID: <295CC5EB4257D411B34D00D0B7748F4432E17E@baldar.brc.mcw.edu> Hi Mark, I noticed that the BioMOBY gbrowse client at the BioMOBY website is down (5:30 pm EST US). My local MOBY Central is also timing out with the following error. "the namespace *** does not exist in the MOBY namespace ontology". I assume that the local MOBY Central we have uses the Ontology Server which is not local. How to resolve this issue? -Vijay Vijay Narayanasamy Bioinformatics Project Programmer and Analyst Human and Molecular Genetics Center Medical College of Wisconsin 8701, W. Watertown Plank Road Milwaukee, WI 53226 414-456-8026 vnarayan@mcw.edu http://brc.mcw.edu/ From markw at illuminae.com Fri Jul 23 19:00:46 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Fri Jul 23 19:02:25 2004 Subject: [MISC] [MOBY-l] BioMOBY Service Failure In-Reply-To: <295CC5EB4257D411B34D00D0B7748F4432E17E@baldar.brc.mcw.edu> References: <295CC5EB4257D411B34D00D0B7748F4432E17E@baldar.brc.mcw.edu> Message-ID: <1090623645.1973.80.camel@myhost.mydomain> Yeah, it looks like the entire machine is down. I am unable to SSH to it either. I have sent a heads-up to the sysadmin, but he is 6119km away from here, and three time zones, so it might not get attended to until Monday. :-( In a couple of days I am going to set up a readonly mirror of MOBY Central here in Vancouver on the new IBM server that was awarded to the MOBY project last month, but that machine isn't yet publicly visible, so I haven't done it yet. Planned for next week. M On Fri, 2004-07-23 at 14:25, Vijay Narayanasamy wrote: > Hi Mark, > > I noticed that the BioMOBY gbrowse client at the BioMOBY website is down > (5:30 pm EST US). > > My local MOBY Central is also timing out with the following error. > "the namespace *** does not exist in the MOBY namespace ontology". > > I assume that the local MOBY Central we have uses the Ontology Server which > is not local. How to resolve this issue? > > -Vijay > > > Vijay Narayanasamy > Bioinformatics Project Programmer and Analyst > Human and Molecular Genetics Center > Medical College of Wisconsin > 8701, W. Watertown Plank Road > Milwaukee, WI 53226 > 414-456-8026 > vnarayan@mcw.edu > http://brc.mcw.edu/ > > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From p.lord at russet.org.uk Tue Jul 27 10:56:35 2004 From: p.lord at russet.org.uk (Phillip Lord) Date: Tue Jul 27 11:01:30 2004 Subject: [MOBY-l] ISMB and service ontologies Message-ID: Dear all Is anyone involved with the moby service ontology going to be at ISMB this year? If so it might be good to talk at some stage. Cheers Phil -- Phillip Lord, Phone: +44 (0) 161 275 6139 PostDoctoral Research Associate, Email: p.lord@russet.org.uk Department of Computer Science http://www.russet.org.uk Kilburn Building http://www.cs.man.ac.uk/~phillord University of Manchester Oxford Road Manchester M13 9PL From bmg at sfu.ca Wed Jul 28 23:15:41 2004 From: bmg at sfu.ca (Benjamin Good) Date: Wed Jul 28 23:16:29 2004 Subject: [MOBY-l] An Ontology question In-Reply-To: References: <410027BE.7050303@sfu.ca> Message-ID: <41086BDD.1040704@sfu.ca> Here is my brain dump for the day. Hope you have time to have a look and correct my misunderstandings :) I guess maybe I'm a bit confused about the definition of "datatype" as it is used within the Moby world. If datatype refers simply to the structure and components of the objects, then why are there datatypes in the ontology that differ in their name but actually have exactly the same structure? For example from the ontology, phenotype_description isa object and hasa String (named Phenotype) and Interactor isa Object and hasa String (named role). Clearly it is useful to be able to determine that a service operates on a "Phenotype" string and not a "role" string because it enables service discovery. For these particular objects, this semantic information is encoded only in the names of the objects. If the ontology was richer, perhaps the semantics could be spread across relationships between terms. As I understand it, it is only really at the service discovery stage that semantics become important. With (hopefully) thousands of services out there, the appropriate selection of services is made possible by understanding the inputs and the outputs at a semantic level. The descriptions of these inputs and outputs could be stored in the objects themselves (as I have been envisioning), in the service ontology (as perhaps most others have already been thinking?), or (what do you think of this?) perhaps additionally through cross-references stored in the definitions of the services. For example, when a service operates on a specific class of data such as gene products ?involved in seed development? that can be specified in an existing external ontology (for example by GO:0048316), the service definition could include a cross-reference to the pertinent node and authority. Such cross-refs would enable the use of external description systems for service discovery and facilitate the intermingling of moby clients with other applications. ? -Ben >>>>>>"Benjamin" == Benjamin Good writes: >>>>>> >>>>>> > > Benjamin> Hello Moby, > > Benjamin> It seems that the moby system would benefit from a > Benjamin> semantically richer object ontology. Has anyone thought > Benjamin> about ways to leverage existing ontologies (such as GO) > Benjamin> for this purpose? > > Benjamin> curious to hear your thoughts > > >Well, GO itself describes the wrong thing, I think. MOBY needs an >ontology of datatypes, and analyses. > > From hudsont at uncw.edu Thu Jul 29 15:51:24 2004 From: hudsont at uncw.edu (Hudson, Thomas C.) Date: Thu Jul 29 15:52:50 2004 Subject: [MOBY-l] A simpler Ontology question Message-ID: <46F56ACD52BC5F4F911EF9C4264FB464967D91@UNCWMAILVS1.dcs.uncw.edu> Here's a simpler question about the ontology I don't understand: As far as I can see, the root of the sequence hierarchy is the VirtualSequence, which is a MOBY object with an integer Length. So there's no way to have a sequence object without the length attached? Tom, who has a database that doesn't store length, meaning length is expensive, and wants to just use accession numbers out of the first database to do lookups in another database, meaning length is unnecessary. From markw at illuminae.com Thu Jul 29 16:03:10 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Thu Jul 29 16:05:02 2004 Subject: [MISC] [MOBY-l] A simpler Ontology question In-Reply-To: <46F56ACD52BC5F4F911EF9C4264FB464967D91@UNCWMAILVS1.dcs.uncw.edu> References: <46F56ACD52BC5F4F911EF9C4264FB464967D91@UNCWMAILVS1.dcs.uncw.edu> Message-ID: <1091131390.22146.129.camel@myhost.mydomain> I'll tackle your question first (sorry Ben), since it is an easier one :-) There are several directions of possible answer to your question, perhaps none of which will please you, but they are the answers: 1) In the current ontology you *cannot* get a child of VirtualSequence that does not have a Length. 2) The ontology is open - if you wish to define a sequence object that does not carry length, you are free to do so. Length was at the root of the sequence hierarchy to avoid situations where you unexpectedly find yourself downloading the entirety of Chromosome 1, and all of its subparts, from genbank because you simply chose to get the sequences of a lists of gi numbers. Retrieving the VirtualSequence object first allows you to do a quick check of whether the sequences you are about to retrieve are of a reasonable size (big or small), and then only submit your query for the "real" data when you have done this pre-screening. (it was also based in the desire to be somewhat like BioPerl, where there are sequence objects that have only length - it just seemed like a good idea at the time) 3) It isn't difficult to determine the length of a string... I don't know if I agree with your assessment that it is "expensive" to compute the size of a sequence. The length field in the object does add a bit of message-size overhead, but it is minor compared to the sequence itself. 4) We also have a FASTA object, if that fits your needs better, which is just straight text. Your choice among these options is entirely up to you. I am always loathe to design new objects that are effectively identical to existing objects, because that is what got us into the state of non-interoperability that we are already in! I would argue that interoperability demands sacrifice... and if that means adding a line to a script to calculate the length of a string, then that is a small sacrifice. But again, the ontologies are open, and you are free to register whatever objects you wish :-) Cheers! M On Thu, 2004-07-29 at 12:51, Hudson, Thomas C. wrote: > Here's a simpler question about the ontology I don't understand: > As far as I can see, the root of the sequence hierarchy is the > VirtualSequence, which is a MOBY object with an integer Length. So > there's no way to have a sequence object without the length attached? > > Tom, who has a database that doesn't store length, meaning length is > expensive, and wants to just use accession numbers out of the first > database to do lookups in another database, meaning length is > unnecessary. > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From gordonp at cbr.nrc.ca Thu Jul 29 16:24:04 2004 From: gordonp at cbr.nrc.ca (Paul Gordon) Date: Thu Jul 29 16:25:28 2004 Subject: [MISC] [MOBY-l] A simpler Ontology question In-Reply-To: <1091131390.22146.129.camel@myhost.mydomain> References: <46F56ACD52BC5F4F911EF9C4264FB464967D91@UNCWMAILVS1.dcs.uncw.edu> <1091131390.22146.129.camel@myhost.mydomain> Message-ID: <41095CE4.1070301@cbr.nrc.ca> The message size increases by log base 10 of the number of course, and length calculation is at worst case linear, a small sacrifice my any computer algorithm measure. :-) >I would argue that interoperability demands sacrifice... and if that >means adding a line to a script to calculate the length of a string, >then that is a small sacrifice. > From michael at acutrans.net Fri Jul 30 15:54:01 2004 From: michael at acutrans.net (Michael Jensen) Date: Fri Jul 30 15:55:29 2004 Subject: [MOBY-l] broken constructing services page... Message-ID: <33C3CA1E-E262-11D8-852E-000393B6201C@acutrans.net> Any Wiki editors: http://biomoby.org/twiki/bin//view/Moby/ConstructingYourService This page seems to be cut off prematurely at the bottom. Can you fix? Thanks!! -Michael Jensen michael@inblosam.com From markw at illuminae.com Fri Jul 30 16:06:53 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Fri Jul 30 16:08:32 2004 Subject: [MISC] [MOBY-l] broken constructing services page... In-Reply-To: <33C3CA1E-E262-11D8-852E-000393B6201C@acutrans.net> References: <33C3CA1E-E262-11D8-852E-000393B6201C@acutrans.net> Message-ID: <1091218013.4541.12.camel@myhost.mydomain> What do you see? It looks correct to me (layout-wise, that is... I can't vouch for its sanity ;-) ) M On Fri, 2004-07-30 at 12:54, Michael Jensen wrote: > Any Wiki editors: > > http://biomoby.org/twiki/bin//view/Moby/ConstructingYourService > > This page seems to be cut off prematurely at the bottom. Can you fix? > > Thanks!! > > -Michael Jensen > michael@inblosam.com > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From gordonp at cbr.nrc.ca Tue Jul 6 11:58:44 2004 From: gordonp at cbr.nrc.ca (Paul Gordon) Date: Tue, 06 Jul 2004 09:58:44 -0600 Subject: [MOBY-l] The fun begins Message-ID: <40EACC34.2060007@cbr.nrc.ca> Hi all, I am reworking the MobyRequest class to work with Apache Axis 1.1beta, since 1.0 has a very crappy ClassLoader that is slowing down my applets by generating 100's of needless HTTP requests. While doing this, I'm trying to make sure I parse SOAP messages as generically as possible. The following is the first of several quirks I'm finding in almost all services: The SOAP response is getting the namespace http://biomoby.org/ rather than http://www.biomoby.org/moby as specified in the API for all the rest of the markup. Is the envelope node (or nodes since sometimes the xxxResponse is wrapped in a xxxReturn) meant to be in a separate namespace from the contents? If so, shouldn't we call it something like http://biomoby.org/transport for clarity's sake? From barbara.re at studenti.unicam.it Tue Jul 6 13:39:12 2004 From: barbara.re at studenti.unicam.it (RE BARBARA) Date: Tue, 6 Jul 2004 19:39:12 +0200 Subject: [MOBY-l] request about getNamespace() in MobyData Message-ID: <1089135552.40eae3c0aa2a3@mail.studenti.unicam.it> Hi, once extract the input of a service (through the Bees java), as can I do for extracting, for examples, the Data Type or Namespaces? I don't succeed in using the method "getNamespaces()" or "getDataType()" because the method getPrimaryInputs() returns me a type MobyData while the methods "getNamespaces()" or "getDataType()" require MobyPrimaryDataSimple. How can I do? Barbara From senger at ebi.ac.uk Tue Jul 6 20:42:14 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 7 Jul 2004 01:42:14 +0100 (BST) Subject: [MOBY-l] request about getNamespace() in MobyData In-Reply-To: <1089135552.40eae3c0aa2a3@mail.studenti.unicam.it> References: <1089135552.40eae3c0aa2a3@mail.studenti.unicam.it> Message-ID: <23733.202.123.48.250.1089160934.squirrel@webmail.ebi.ac.uk> Hi, Please forgive me if I has not understood correctly your question, but if I have then here is an answer: > I don't succeed in using the method "getNamespaces()" or "getDataType()" > because the method getPrimaryInputs() returns me a type MobyData while the > methods "getNamespaces()" or "getDataType()" require > MobyPrimaryDataSimple. > MobyPrimaryDataSimple inherits from MobyData. So, actually,the method getPrimaryInputs() only seems to return MobyData but in fact it returns more specific type, e.g. MobyPrimaryDataSimple. So, just cast it. Regards, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From mwilkinson at mrl.ubc.ca Mon Jul 12 02:35:43 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Sun, 11 Jul 2004 23:35:43 -0700 Subject: [MOBY-l] Cleaning up the MOBY Central registry Message-ID: <1089614143.1823.35.camel@myhost.mydomain> Hi all, I want to clean up the registry now that there is a separate test registry up and running. The following services seem to be "litter" (folks at IRRI - can you confirm/deny this for your services?). unless I hear otherwise I will delete them from the registry in the next few days. +--------------------------+----------------------+ | servicename | authority_uri | +--------------------------+----------------------+ | test3_SequenceToFASTA | ccgb.umn.edu | | test_getgermplasm | www.iris.irri.org | | test_getgermplasm_wtrait | www.iris.irri.org | | test_getstudy | www.iris.irri.org | | test_gettrait | www.iris.irri.org | | test_SequenceToFASTA | ccgb.umn.edu | | test_SequenceToFASTA | cilantro.bio.unc.edu | | test_u26230 | mobyed1.sdsc.edu | +--------------------------+----------------------+ Cheers! M -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From mwilkinson at mrl.ubc.ca Mon Jul 12 02:37:56 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Sun, 11 Jul 2004 23:37:56 -0700 Subject: [MOBY-l] cleaning up the ontologies Message-ID: <1089614276.1823.37.camel@myhost.mydomain> Hi again, The same goes for these objects (yeah, I see some of my own are in there as well...) +----------------------------------+-------------------+---------------------+ | object_type | authority | contact_email | +----------------------------------+-------------------+---------------------+ | TEST | www.sdsc.edu | steube at sdsc.edu | | testString | www.illuminae.com | markw at illuminae.com | | test2String | www.illuminae.com | markw at illuminae.com | | MyTestingDataType_10809965326221 | testing.org | mail at mail.com | | testout | www.iris.irri.org | mulat at cgiar.org | +----------------------------------+-------------------+---------------------+ Unless I hear otherwise I will delete these in the next few days. M -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From bmg at sfu.ca Thu Jul 22 16:46:54 2004 From: bmg at sfu.ca (Benjamin Good) Date: Fri, 23 Jul 2004 04:46:54 +0800 Subject: [MOBY-l] An Ontology question Message-ID: <410027BE.7050303@sfu.ca> Hello Moby, It seems that the moby system would benefit from a semantically richer object ontology. Has anyone thought about ways to leverage existing ontologies (such as GO) for this purpose? curious to hear your thoughts -Ben From p.lord at russet.org.uk Wed Jul 21 10:28:10 2004 From: p.lord at russet.org.uk (Phillip Lord) Date: 21 Jul 2004 15:28:10 +0100 Subject: [MOBY-l] An Ontology question In-Reply-To: <410027BE.7050303@sfu.ca> References: <410027BE.7050303@sfu.ca> Message-ID: >>>>> "Benjamin" == Benjamin Good writes: Benjamin> Hello Moby, Benjamin> It seems that the moby system would benefit from a Benjamin> semantically richer object ontology. Has anyone thought Benjamin> about ways to leverage existing ontologies (such as GO) Benjamin> for this purpose? Benjamin> curious to hear your thoughts Well, GO itself describes the wrong thing, I think. MOBY needs an ontology of datatypes, and analyses. Several groups are thinking about producing semantically richer ontologies. Within the mygrid project (www.mygrid.org.uk) we have a fairly rich ontology (although possibly it's too rich!). Steffen Moeller has also developed a small service ontology, and the moby ontology is being worked on. I'm hoping that we can all get together on this and work together to generate a service ontology with good coverage, good usability, and clear semantics. Lots of scope for pub/restaurant discussions at ISMB, for those who are going to be there. If there is interest outside the people that I've already mentioned, then we should organise a small meeting (or "BOF" as people will insist on calling them). Cheers Phil From fgibbons at hms.harvard.edu Wed Jul 21 11:05:04 2004 From: fgibbons at hms.harvard.edu (Frank Gibbons) Date: Wed, 21 Jul 2004 11:05:04 -0400 Subject: [MOBY-l] An Ontology question In-Reply-To: <410027BE.7050303@sfu.ca> Message-ID: <5.2.1.1.2.20040721105107.01a031c8@email.med.harvard.edu> Hi Ben, I've been thinking about ways to extend the object (and service) ontology. In fact, as part of the BioGraphNet project for exchanging protein/genetic interaction networks (http://biographnet.sourceforge.net), Gabriel Berriz and I have added an 'interaction_partner' object, and then extended it with terms from the Proteomics Standards Initiative - Molecular Interaction (PSI-MI) controlled vocabulary for interaction_detection, at least to the first two levels. Since this is development work so far, most of these changes have been made in the test Registry that Mark put up a few weeks ago, not in the 'real' registry. So far, we've done this by hand, but clearly it would make much more sense to either automate it, or better yet, find a way to link from MOBY's object registry to a URI of PSI-MI's. Unfortunately, being an RDF newbie, I'm not really sure of the best way to do this, or even if it's possible. I know that Mark W. is meeting with the myGRID folks this summer, to discuss ways to re-use their massive ontology, so that may obviate any other plans. It strikes me that it might not be desirable to include any ontology in all of its gory detail, at least in the absence of appropriate tools to navigate and visualise MOBY's ontologies. Martin Senger has written some really useful tools for that, but they generate static images rather than interactive ones, so once below the spatial resolution of your printer/screen, it's not possible to read it, and it's close to that right now. Just a brain dump. What are you thinking? -Frank At 04:46 PM 7/22/2004, Benjamin Good wrote: >Hello Moby, > >It seems that the moby system would benefit from a semantically richer >object ontology. Has anyone thought about ways to leverage existing >ontologies (such as GO) for this purpose? > >curious to hear your thoughts >-Ben > > > >_______________________________________________ >moby-l mailing list >moby-l at biomoby.org >http://biomoby.org/mailman/listinfo/moby-l PhD, Computational Biologist, Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA. Tel: 617-432-3555 Fax: 617-432-3557 http://llama.med.harvard.edu/~fgibbons From p.lord at russet.org.uk Wed Jul 21 11:42:58 2004 From: p.lord at russet.org.uk (Phillip Lord) Date: 21 Jul 2004 16:42:58 +0100 Subject: [MOBY-l] An Ontology question In-Reply-To: <5.2.1.1.2.20040721105107.01a031c8@email.med.harvard.edu> References: <5.2.1.1.2.20040721105107.01a031c8@email.med.harvard.edu> Message-ID: >>>>> "Frank" == Frank Gibbons writes: Frank> So far, we've done this by hand, but clearly it would make Frank> much more sense to either automate it, or better yet, find a Frank> way to link from MOBY's object registry to a URI of Frank> PSI-MI's. Unfortunately, being an RDF newbie, I'm not really Frank> sure of the best way to do this, or even if it's possible. I Frank> know that Mark W. is meeting with the myGRID folks this Frank> summer, to discuss ways to re-use their massive ontology, so Frank> that may obviate any other plans. Frank> It strikes me that it might not be desirable to include any Frank> ontology in all of its gory detail, at least in the absence Frank> of appropriate tools to navigate and visualise MOBY's Frank> ontologies. Martin Senger has written some really useful Frank> tools for that, but they generate static images rather than Frank> interactive ones, so once below the spatial resolution of Frank> your printer/screen, it's not possible to read it, and it's Frank> close to that right now. One of the issues with any complex ontology is how to visualise it, and how to present it to the different kinds of user who might want to use it. Within GO, for example, the annotators, GO curators and end users all seem the same ontology. But its doesn't necessarily need to be this way. (Indeed GO slims are an acknowledgement of this). I think that mygrid ontology is too complex to present to the end user, per se, but having a layer which removes most of the complexity for display, well still leaving this complexity so that the underlying machinery can use it seems like a good approach. Personally I would like to realise the mygrid ontology in a number of inter-related forms; the idea would be to have an underlying OWL-DL based ontology (so that we can use reasoner support, which helps in the building of the ontology). Then we use this to generate representationally simpler ontologies. So a stripped down OBO style ontology (modelled as a DAG). Moby-s would probably need something half way in between--it needs data type information (sequence has-a string) in the ontology which would probably be out of place in a OBO ontology. So you'd have to add something back in. All of which makes development of the ontology somewhat more complex, but will, hopefully, make it easier for the end user. Which is probably the way that it should be. I managed to talk with Steffen about this earlier in the month, and should get a chance to talk with Mark at ISMB. I guess we should try and advertise a meeting as a BOF, as it looks like others might be interested. Incidentally, for those of you going to ISMB, who are interested in ontologies, I have to say, in an entirely unbiased manner, that the bio-ontologies SIG (http://bio-ontologies.man.ac.uk/) looks wonderful. Everyone should attend! Cheers Phil From lstein at cshl.edu Thu Jul 22 18:16:51 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Thu, 22 Jul 2004 18:16:51 -0400 Subject: [MOBY-l] My fortune for the day Message-ID: <200407221816.51892.lstein@cshl.edu> Hi Folks, My /usr/bin/fortune program popped up the following gem this evening: Oh Lord, won't you buy me a 4BSD? My friends all got sources, so why can't I see? Come all you moby hackers, come sing it out with me: To hell with the lawyers from AT&T! Amazing. Lincoln -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From edoneel at sdf.lonestar.org Fri Jul 23 05:52:47 2004 From: edoneel at sdf.lonestar.org (Bruce O'Neel) Date: Fri, 23 Jul 2004 09:52:47 +0000 Subject: [MOBY-l] My fortune for the day In-Reply-To: <200407221816.51892.lstein@cshl.edu> References: <200407221816.51892.lstein@cshl.edu> Message-ID: <20040723095247.GB12415@SDF.LONESTAR.ORG> For those of you who might not know: http://www.clueless.com/jargon3.0.0/moby.html A title of address (never of third-person reference), usually used to show admiration, respect, and/or friendliness to a competent hacker. "Greetings, moby Dave. How's that address-book thing for the Mac going?" On Thu, Jul 22, 2004 at 06:16:51PM -0400, Lincoln Stein wrote: > Hi Folks, > > My /usr/bin/fortune program popped up the following gem this evening: > > Oh Lord, won't you buy me a 4BSD? > My friends all got sources, so why can't I see? > Come all you moby hackers, come sing it out with me: > To hell with the lawyers from AT&T! > > Amazing. > > Lincoln > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- edoneel at sdf.lonestar.org SDF Public Access UNIX System - http://sdf.lonestar.org From p.lord at russet.org.uk Fri Jul 23 06:33:14 2004 From: p.lord at russet.org.uk (Phillip Lord) Date: 23 Jul 2004 11:33:14 +0100 Subject: [MOBY-l] My fortune for the day In-Reply-To: <200407221816.51892.lstein@cshl.edu> References: <200407221816.51892.lstein@cshl.edu> Message-ID: >>>>> "Lincoln" == Lincoln Stein writes: Lincoln> Hi Folks, Lincoln> My /usr/bin/fortune program popped up the following gem Lincoln> this evening: Lincoln> Oh Lord, won't you buy me a 4BSD? My friends all got Lincoln> sources, so why can't I see? Come all you moby Lincoln> hackers, come sing it out with me: To hell with the Lincoln> lawyers from AT&T! Lincoln> Amazing. If only Janis were still here to sing it..... Cheers Phil From lstein at cshl.edu Fri Jul 23 10:44:37 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Fri, 23 Jul 2004 10:44:37 -0400 Subject: [MOBY-l] My fortune for the day In-Reply-To: <20040723095247.GB12415@SDF.LONESTAR.ORG> References: <200407221816.51892.lstein@cshl.edu> <20040723095247.GB12415@SDF.LONESTAR.ORG> Message-ID: <200407231044.37043.lstein@cshl.edu> Bruce, thanks for the jargon pointer. I never knew that. I'm particularly intrigued about the old-style moby factor. By that definition, my current desktop machine has 116 micro-mobies. Lincoln On Friday 23 July 2004 05:52 am, Bruce O'Neel wrote: > For those of you who might not know: > > http://www.clueless.com/jargon3.0.0/moby.html > > A title of address (never of third-person reference), usually used to > show admiration, respect, and/or friendliness to a competent > hacker. "Greetings, moby Dave. How's that address-book thing for the > Mac going?" > > On Thu, Jul 22, 2004 at 06:16:51PM -0400, Lincoln Stein wrote: > > Hi Folks, > > > > My /usr/bin/fortune program popped up the following gem this evening: > > > > Oh Lord, won't you buy me a 4BSD? > > My friends all got sources, so why can't I see? > > Come all you moby hackers, come sing it out with me: > > To hell with the lawyers from AT&T! > > > > Amazing. > > > > Lincoln > > > > -- > > Lincoln D. Stein > > Cold Spring Harbor Laboratory > > 1 Bungtown Road > > Cold Spring Harbor, NY 11724 > > _______________________________________________ > > moby-l mailing list > > moby-l at biomoby.org > > http://biomoby.org/mailman/listinfo/moby-l -- Lincoln Stein lstein at cshl.edu Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) From VNarayan at mail.brc.mcw.edu Fri Jul 23 17:25:20 2004 From: VNarayan at mail.brc.mcw.edu (Vijay Narayanasamy) Date: Fri, 23 Jul 2004 16:25:20 -0500 Subject: [MOBY-l] BioMOBY Service Failure Message-ID: <295CC5EB4257D411B34D00D0B7748F4432E17E@baldar.brc.mcw.edu> Hi Mark, I noticed that the BioMOBY gbrowse client at the BioMOBY website is down (5:30 pm EST US). My local MOBY Central is also timing out with the following error. "the namespace *** does not exist in the MOBY namespace ontology". I assume that the local MOBY Central we have uses the Ontology Server which is not local. How to resolve this issue? -Vijay Vijay Narayanasamy Bioinformatics Project Programmer and Analyst Human and Molecular Genetics Center Medical College of Wisconsin 8701, W. Watertown Plank Road Milwaukee, WI 53226 414-456-8026 vnarayan at mcw.edu http://brc.mcw.edu/ From markw at illuminae.com Fri Jul 23 19:00:46 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 23 Jul 2004 16:00:46 -0700 Subject: [MISC] [MOBY-l] BioMOBY Service Failure In-Reply-To: <295CC5EB4257D411B34D00D0B7748F4432E17E@baldar.brc.mcw.edu> References: <295CC5EB4257D411B34D00D0B7748F4432E17E@baldar.brc.mcw.edu> Message-ID: <1090623645.1973.80.camel@myhost.mydomain> Yeah, it looks like the entire machine is down. I am unable to SSH to it either. I have sent a heads-up to the sysadmin, but he is 6119km away from here, and three time zones, so it might not get attended to until Monday. :-( In a couple of days I am going to set up a readonly mirror of MOBY Central here in Vancouver on the new IBM server that was awarded to the MOBY project last month, but that machine isn't yet publicly visible, so I haven't done it yet. Planned for next week. M On Fri, 2004-07-23 at 14:25, Vijay Narayanasamy wrote: > Hi Mark, > > I noticed that the BioMOBY gbrowse client at the BioMOBY website is down > (5:30 pm EST US). > > My local MOBY Central is also timing out with the following error. > "the namespace *** does not exist in the MOBY namespace ontology". > > I assume that the local MOBY Central we have uses the Ontology Server which > is not local. How to resolve this issue? > > -Vijay > > > Vijay Narayanasamy > Bioinformatics Project Programmer and Analyst > Human and Molecular Genetics Center > Medical College of Wisconsin > 8701, W. Watertown Plank Road > Milwaukee, WI 53226 > 414-456-8026 > vnarayan at mcw.edu > http://brc.mcw.edu/ > > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From p.lord at russet.org.uk Tue Jul 27 10:56:35 2004 From: p.lord at russet.org.uk (Phillip Lord) Date: 27 Jul 2004 15:56:35 +0100 Subject: [MOBY-l] ISMB and service ontologies Message-ID: Dear all Is anyone involved with the moby service ontology going to be at ISMB this year? If so it might be good to talk at some stage. Cheers Phil -- Phillip Lord, Phone: +44 (0) 161 275 6139 PostDoctoral Research Associate, Email: p.lord at russet.org.uk Department of Computer Science http://www.russet.org.uk Kilburn Building http://www.cs.man.ac.uk/~phillord University of Manchester Oxford Road Manchester M13 9PL From bmg at sfu.ca Wed Jul 28 23:15:41 2004 From: bmg at sfu.ca (Benjamin Good) Date: Thu, 29 Jul 2004 11:15:41 +0800 Subject: [MOBY-l] An Ontology question In-Reply-To: References: <410027BE.7050303@sfu.ca> Message-ID: <41086BDD.1040704@sfu.ca> Here is my brain dump for the day. Hope you have time to have a look and correct my misunderstandings :) I guess maybe I'm a bit confused about the definition of "datatype" as it is used within the Moby world. If datatype refers simply to the structure and components of the objects, then why are there datatypes in the ontology that differ in their name but actually have exactly the same structure? For example from the ontology, phenotype_description isa object and hasa String (named Phenotype) and Interactor isa Object and hasa String (named role). Clearly it is useful to be able to determine that a service operates on a "Phenotype" string and not a "role" string because it enables service discovery. For these particular objects, this semantic information is encoded only in the names of the objects. If the ontology was richer, perhaps the semantics could be spread across relationships between terms. As I understand it, it is only really at the service discovery stage that semantics become important. With (hopefully) thousands of services out there, the appropriate selection of services is made possible by understanding the inputs and the outputs at a semantic level. The descriptions of these inputs and outputs could be stored in the objects themselves (as I have been envisioning), in the service ontology (as perhaps most others have already been thinking?), or (what do you think of this?) perhaps additionally through cross-references stored in the definitions of the services. For example, when a service operates on a specific class of data such as gene products ?involved in seed development? that can be specified in an existing external ontology (for example by GO:0048316), the service definition could include a cross-reference to the pertinent node and authority. Such cross-refs would enable the use of external description systems for service discovery and facilitate the intermingling of moby clients with other applications. ? -Ben >>>>>>"Benjamin" == Benjamin Good writes: >>>>>> >>>>>> > > Benjamin> Hello Moby, > > Benjamin> It seems that the moby system would benefit from a > Benjamin> semantically richer object ontology. Has anyone thought > Benjamin> about ways to leverage existing ontologies (such as GO) > Benjamin> for this purpose? > > Benjamin> curious to hear your thoughts > > >Well, GO itself describes the wrong thing, I think. MOBY needs an >ontology of datatypes, and analyses. > > From hudsont at uncw.edu Thu Jul 29 15:51:24 2004 From: hudsont at uncw.edu (Hudson, Thomas C.) Date: Thu, 29 Jul 2004 15:51:24 -0400 Subject: [MOBY-l] A simpler Ontology question Message-ID: <46F56ACD52BC5F4F911EF9C4264FB464967D91@UNCWMAILVS1.dcs.uncw.edu> Here's a simpler question about the ontology I don't understand: As far as I can see, the root of the sequence hierarchy is the VirtualSequence, which is a MOBY object with an integer Length. So there's no way to have a sequence object without the length attached? Tom, who has a database that doesn't store length, meaning length is expensive, and wants to just use accession numbers out of the first database to do lookups in another database, meaning length is unnecessary. From markw at illuminae.com Thu Jul 29 16:03:10 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 29 Jul 2004 13:03:10 -0700 Subject: [MISC] [MOBY-l] A simpler Ontology question In-Reply-To: <46F56ACD52BC5F4F911EF9C4264FB464967D91@UNCWMAILVS1.dcs.uncw.edu> References: <46F56ACD52BC5F4F911EF9C4264FB464967D91@UNCWMAILVS1.dcs.uncw.edu> Message-ID: <1091131390.22146.129.camel@myhost.mydomain> I'll tackle your question first (sorry Ben), since it is an easier one :-) There are several directions of possible answer to your question, perhaps none of which will please you, but they are the answers: 1) In the current ontology you *cannot* get a child of VirtualSequence that does not have a Length. 2) The ontology is open - if you wish to define a sequence object that does not carry length, you are free to do so. Length was at the root of the sequence hierarchy to avoid situations where you unexpectedly find yourself downloading the entirety of Chromosome 1, and all of its subparts, from genbank because you simply chose to get the sequences of a lists of gi numbers. Retrieving the VirtualSequence object first allows you to do a quick check of whether the sequences you are about to retrieve are of a reasonable size (big or small), and then only submit your query for the "real" data when you have done this pre-screening. (it was also based in the desire to be somewhat like BioPerl, where there are sequence objects that have only length - it just seemed like a good idea at the time) 3) It isn't difficult to determine the length of a string... I don't know if I agree with your assessment that it is "expensive" to compute the size of a sequence. The length field in the object does add a bit of message-size overhead, but it is minor compared to the sequence itself. 4) We also have a FASTA object, if that fits your needs better, which is just straight text. Your choice among these options is entirely up to you. I am always loathe to design new objects that are effectively identical to existing objects, because that is what got us into the state of non-interoperability that we are already in! I would argue that interoperability demands sacrifice... and if that means adding a line to a script to calculate the length of a string, then that is a small sacrifice. But again, the ontologies are open, and you are free to register whatever objects you wish :-) Cheers! M On Thu, 2004-07-29 at 12:51, Hudson, Thomas C. wrote: > Here's a simpler question about the ontology I don't understand: > As far as I can see, the root of the sequence hierarchy is the > VirtualSequence, which is a MOBY object with an integer Length. So > there's no way to have a sequence object without the length attached? > > Tom, who has a database that doesn't store length, meaning length is > expensive, and wants to just use accession numbers out of the first > database to do lookups in another database, meaning length is > unnecessary. > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From gordonp at cbr.nrc.ca Thu Jul 29 16:24:04 2004 From: gordonp at cbr.nrc.ca (Paul Gordon) Date: Thu, 29 Jul 2004 14:24:04 -0600 Subject: [MISC] [MOBY-l] A simpler Ontology question In-Reply-To: <1091131390.22146.129.camel@myhost.mydomain> References: <46F56ACD52BC5F4F911EF9C4264FB464967D91@UNCWMAILVS1.dcs.uncw.edu> <1091131390.22146.129.camel@myhost.mydomain> Message-ID: <41095CE4.1070301@cbr.nrc.ca> The message size increases by log base 10 of the number of course, and length calculation is at worst case linear, a small sacrifice my any computer algorithm measure. :-) >I would argue that interoperability demands sacrifice... and if that >means adding a line to a script to calculate the length of a string, >then that is a small sacrifice. > From michael at acutrans.net Fri Jul 30 15:54:01 2004 From: michael at acutrans.net (Michael Jensen) Date: Fri, 30 Jul 2004 15:54:01 -0400 Subject: [MOBY-l] broken constructing services page... Message-ID: <33C3CA1E-E262-11D8-852E-000393B6201C@acutrans.net> Any Wiki editors: http://biomoby.org/twiki/bin//view/Moby/ConstructingYourService This page seems to be cut off prematurely at the bottom. Can you fix? Thanks!! -Michael Jensen michael at inblosam.com From markw at illuminae.com Fri Jul 30 16:06:53 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 30 Jul 2004 13:06:53 -0700 Subject: [MISC] [MOBY-l] broken constructing services page... In-Reply-To: <33C3CA1E-E262-11D8-852E-000393B6201C@acutrans.net> References: <33C3CA1E-E262-11D8-852E-000393B6201C@acutrans.net> Message-ID: <1091218013.4541.12.camel@myhost.mydomain> What do you see? It looks correct to me (layout-wise, that is... I can't vouch for its sanity ;-) ) M On Fri, 2004-07-30 at 12:54, Michael Jensen wrote: > Any Wiki editors: > > http://biomoby.org/twiki/bin//view/Moby/ConstructingYourService > > This page seems to be cut off prematurely at the bottom. Can you fix? > > Thanks!! > > -Michael Jensen > michael at inblosam.com > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre