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From: Hilmar L. <hl...@ne...> - 2013-07-23 12:02:29
|
FYI. This may well be worth looking at if the scope suggests reusing it for describing substitution models. -hilmar Sent with a tap. Begin forwarded message: > From: Nicolas Le Novere <n.l...@gm...> > Date: July 20, 2013 12:45:58 AM GMT+02:00 > To: "obo...@li..." <obo...@li...> > Subject: [Obo-discuss] Mathematical Modelling Ontology (MAMO) > Reply-To: n.l...@gm..., obo...@li... > > Hello, > > As per the requirements listed at: > http://code.google.com/p/obo-foundry-operations-committee/wiki/Policy_for_OBO_namespace_and_associated_PURL_requests > > We would like to announce the birth of a new ontology.The Mathematical > Modelling Ontology (MAMO) aims to be a classification of the types of > mathematical models used mostly in the life sciences, their variables, > relationships and other relevant features. > > More information is available at > http://sourceforge.net/p/mamo-ontology/wiki/Home/ > > Discussion about the ontology can take place at: > http://sourceforge.net/p/mamo-ontology/discussion/ > > Term requests can be filed at: > http://sourceforge.net/p/mamo-ontology/tickets/ > > Best regards > > -- > Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT > Tel: +441223496433 Mob:+447833147074 n.l...@gm... > orcid.org//0000-0002-6309-7327 http://lenoverelab.org/perso/lenov/ > Skype:n.lenovere twitter:@lenovere http://nlenov.wordpress.com/ > > > > > ------------------------------------------------------------------------------ > See everything from the browser to the database with AppDynamics > Get end-to-end visibility with application monitoring from AppDynamics > Isolate bottlenecks and diagnose root cause in seconds. > Start your free trial of AppDynamics Pro today! > http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk > _______________________________________________ > Obo-discuss mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-discuss -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
From: Arlin S. <ar...@um...> - 2013-07-02 19:04:19
|
I think "render anchor" captures the needed concept more clearly. Another option is to allow node A is_root_of tree B but assign it 0 confidence. It is important to note that the issue Ben raises has existed for decades. It would be great to solve this problem in a way that is consistent with current practices and expectations, but I'm not sure exactly what they are. My impression is that systematists tend to be more careful about designating outgroups, whereas molecular evolutionists and others produce unrooted trees and depict them as rooted trees without thinking about it too much (most molecular phylogenies are inferred using time-symmetric models, so they are not rooted). Some software uses a 3-way basal polytomy as a cryptic signal that the tree is unrooted. Alas, this cryptically unrooted tree is indistinguishable from a rooted tree with a 3-way basal polytomy. Other software may use [&U] and [&R]. Arlin On Jun 30, 2013, at 9:58 PM, Matt Yoder wrote: > It sounds like this concept is specifically (only?) used for > rendering? How about making it specific and calling it a "render > anchor" or some such? > > Cheers, > Matt > > On Sat, Jun 29, 2013 at 5:03 PM, Ben Morris <be...@be...> wrote: >> A few of us discussed this briefly at iEvoBio; it would be great to >> have a concept similar to "has_Root", but for unrooted trees. Some >> tree formats, such as Newick, represent rooted and unrooted trees >> identically - an unrooted tree has a "pseudo-root" and is represented >> the same way as a rooted tree. The position of this pseudo-root is >> completely arbitrary. If a Newick tree is converted to CDAO and then >> back to Newick, the resulting tree may appear to be "rooted" >> differently than the original. While this is technically fine (since >> it's unrooted, it shouldn't matter where the "pseudo-root" is placed), >> it may be confusing or irritating to users. Having a property >> cdao:has_PseudoRoot would ensure that the tree could be retrieved from >> a triple store and converted back to a Newick tree without changing >> the position of the pseudo-root - so users would get back a tree that >> they could easily verify was identical to what they started with. >> >> Currently I'm using has_Root for unrooted trees; this is certainly >> incorrect, as the pseudo-root is not a root. It's important to >> distinguish between a true root and what's merely a starting point for >> convenience but has no real meaning. >> >> >> Ben Morris >> PhD student, Ecology/Evolutionary Biology >> University of North Carolina, Chapel Hill, NC >> Mail: be...@be... | Twitter: @bendmorris >> Web: www.bendmorris.com >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by Windows: >> >> Build for Windows Store. >> >> http://p.sf.net/sfu/windows-dev2dev >> _______________________________________________ >> CDAO-discuss mailing list >> CDA...@li... >> https://lists.sourceforge.net/lists/listinfo/cdao-discuss > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Windows: > > Build for Windows Store. > > http://p.sf.net/sfu/windows-dev2dev > _______________________________________________ > CDAO-discuss mailing list > CDA...@li... > https://lists.sourceforge.net/lists/listinfo/cdao-discuss ------- Arlin Stoltzfus (ar...@um...) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD, 20850 tel: 240 314 6208; web: www.molevol.org |
From: Hilmar L. <hl...@ne...> - 2013-07-01 14:25:24
|
Another alternative I was thinking about is capturing the semantics through type rather than property.(*) For example, we could create a class 'pseudo root' ("a node in an unrooted tree that is designated as a root node solely for the purposes of maintaining consistent appearance when rendering the tree graphically or in parenthetical formats, such as Newick, that do not allow distinction of rooted from unrooted trees"), rdf:type the respective node that way (in addition to rdf:type cdao:Node), and then associate the node to the tree with something as neutral as "bfo:has part", or "cdao:has". A SPARQL query would then extract the node using the rdf:type triple. -hilmar (*) It's worth keeping in mind that while there is a natural-language temptation to put lots of differentiation into the property, reasoners can do very little with properties, beyond inferring other properties based on subproperty, property chains, inverse etc assertions. Type hierarchies typically yield a lot more in terms of richness of reasoning than a proliferation of properties does. On Jun 30, 2013, at 9:58 PM, Matt Yoder wrote: > It sounds like this concept is specifically (only?) used for > rendering? How about making it specific and calling it a "render > anchor" or some such? > > Cheers, > Matt > > On Sat, Jun 29, 2013 at 5:03 PM, Ben Morris <be...@be...> wrote: >> A few of us discussed this briefly at iEvoBio; it would be great to >> have a concept similar to "has_Root", but for unrooted trees. Some >> tree formats, such as Newick, represent rooted and unrooted trees >> identically - an unrooted tree has a "pseudo-root" and is represented >> the same way as a rooted tree. The position of this pseudo-root is >> completely arbitrary. If a Newick tree is converted to CDAO and then >> back to Newick, the resulting tree may appear to be "rooted" >> differently than the original. While this is technically fine (since >> it's unrooted, it shouldn't matter where the "pseudo-root" is placed), >> it may be confusing or irritating to users. Having a property >> cdao:has_PseudoRoot would ensure that the tree could be retrieved from >> a triple store and converted back to a Newick tree without changing >> the position of the pseudo-root - so users would get back a tree that >> they could easily verify was identical to what they started with. >> >> Currently I'm using has_Root for unrooted trees; this is certainly >> incorrect, as the pseudo-root is not a root. It's important to >> distinguish between a true root and what's merely a starting point for >> convenience but has no real meaning. >> >> >> Ben Morris >> PhD student, Ecology/Evolutionary Biology >> University of North Carolina, Chapel Hill, NC >> Mail: be...@be... | Twitter: @bendmorris >> Web: www.bendmorris.com >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by Windows: >> >> Build for Windows Store. >> >> http://p.sf.net/sfu/windows-dev2dev >> _______________________________________________ >> CDAO-discuss mailing list >> CDA...@li... >> https://lists.sourceforge.net/lists/listinfo/cdao-discuss > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Windows: > > Build for Windows Store. > > http://p.sf.net/sfu/windows-dev2dev > _______________________________________________ > CDAO-discuss mailing list > CDA...@li... > https://lists.sourceforge.net/lists/listinfo/cdao-discuss -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
From: Matt Y. <dia...@gm...> - 2013-07-01 01:58:43
|
It sounds like this concept is specifically (only?) used for rendering? How about making it specific and calling it a "render anchor" or some such? Cheers, Matt On Sat, Jun 29, 2013 at 5:03 PM, Ben Morris <be...@be...> wrote: > A few of us discussed this briefly at iEvoBio; it would be great to > have a concept similar to "has_Root", but for unrooted trees. Some > tree formats, such as Newick, represent rooted and unrooted trees > identically - an unrooted tree has a "pseudo-root" and is represented > the same way as a rooted tree. The position of this pseudo-root is > completely arbitrary. If a Newick tree is converted to CDAO and then > back to Newick, the resulting tree may appear to be "rooted" > differently than the original. While this is technically fine (since > it's unrooted, it shouldn't matter where the "pseudo-root" is placed), > it may be confusing or irritating to users. Having a property > cdao:has_PseudoRoot would ensure that the tree could be retrieved from > a triple store and converted back to a Newick tree without changing > the position of the pseudo-root - so users would get back a tree that > they could easily verify was identical to what they started with. > > Currently I'm using has_Root for unrooted trees; this is certainly > incorrect, as the pseudo-root is not a root. It's important to > distinguish between a true root and what's merely a starting point for > convenience but has no real meaning. > > > Ben Morris > PhD student, Ecology/Evolutionary Biology > University of North Carolina, Chapel Hill, NC > Mail: be...@be... | Twitter: @bendmorris > Web: www.bendmorris.com > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Windows: > > Build for Windows Store. > > http://p.sf.net/sfu/windows-dev2dev > _______________________________________________ > CDAO-discuss mailing list > CDA...@li... > https://lists.sourceforge.net/lists/listinfo/cdao-discuss |
From: Ben M. <be...@be...> - 2013-06-29 23:00:25
|
A few of us discussed this briefly at iEvoBio; it would be great to have a concept similar to "has_Root", but for unrooted trees. Some tree formats, such as Newick, represent rooted and unrooted trees identically - an unrooted tree has a "pseudo-root" and is represented the same way as a rooted tree. The position of this pseudo-root is completely arbitrary. If a Newick tree is converted to CDAO and then back to Newick, the resulting tree may appear to be "rooted" differently than the original. While this is technically fine (since it's unrooted, it shouldn't matter where the "pseudo-root" is placed), it may be confusing or irritating to users. Having a property cdao:has_PseudoRoot would ensure that the tree could be retrieved from a triple store and converted back to a Newick tree without changing the position of the pseudo-root - so users would get back a tree that they could easily verify was identical to what they started with. Currently I'm using has_Root for unrooted trees; this is certainly incorrect, as the pseudo-root is not a root. It's important to distinguish between a true root and what's merely a starting point for convenience but has no real meaning. Ben Morris PhD student, Ecology/Evolutionary Biology University of North Carolina, Chapel Hill, NC Mail: be...@be... | Twitter: @bendmorris Web: www.bendmorris.com |
From: Hilmar L. <hl...@ne...> - 2013-05-01 22:37:16
|
On Apr 30, 2013, at 2:42 PM, Arlin Stoltzfus wrote: > What would be the representation scheme for putting this in CDAO? The logical place in the current version would be CDAOAnnotation: ModelDescription: SubstitutionModel. But I'm not sure if that part of the class hierarchy is well conceived. I agree, but I also think it's better to have in a reasonable place in the hierarchy for now and rethink that hierarchy later, compared to trying to do both at the same time. Daniel - thanks for forwarding the responses! -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
From: Arlin S. <ar...@um...> - 2013-04-30 18:42:13
|
Sorry for the delayed response. Obviously it would be useful to get this hierarchy into an ontology like CDAO. What would be the representation scheme for putting this in CDAO? The logical place in the current version would be CDAOAnnotation: ModelDescription: SubstitutionModel. But I'm not sure if that part of the class hierarchy is well conceived. Arlin On Apr 5, 2013, at 6:14 PM, Hilmar Lapp wrote: > This is from a post to R-SIG-phylo. What do folks here think about using the following part of the Jmodeltest2 documentation for fleshing out the substitution models section in CDAO? > > https://code.google.com/p/jmodeltest2/wiki/TheoreticalBackground#Hierarchical_Likelihood_Ratio_Tests_(hLRT) > > Daniel - while not the kind of answer you were hoping for, I'd be very appreciative if you could forward to me if you do receive pointers to good sources. FYI, CDAO is the Comparative Data Analysis Ontology (http://www.evolutionaryontology.org/). > > -hilmar > > On Apr 5, 2013, at 12:23 PM, Daniel Barker wrote: > >> Hello, >> >> Is there a review or list of ~every specific nucleotide substitution model >> that has been proposed or used in the literature (with references)? >> >> I'm interested in reversible models. >> >> The most exhaustive list I have is from the jModeltest documentation, >> https://code.google.com/p/jmodeltest2/wiki/TheoreticalBackground#Models_of_ >> nucleotide_substitution >> >> I realise an enormous number of models is possible (and may have been used >> in model averaging). I'm keen to know which have some precedent in the >> literature, along the lines of those listed above. I'm finding it >> difficult to get beyond the standard sources. >> >> Thank you in advance, >> >> Daniel >> >> -- >> Daniel Barker >> http://bio.st-andrews.ac.uk/staff/db60.htm >> The University of St Andrews is a charity registered in Scotland : No >> SC013532 >> >> _______________________________________________ >> R-sig-phylo mailing list - R-s...@r-... >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> Searchable archive at http://www.mail-archive.com/r-s...@r-.../ > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > ------------------------------------------------------------------------------ > Minimize network downtime and maximize team effectiveness. > Reduce network management and security costs.Learn how to hire > the most talented Cisco Certified professionals. Visit the > Employer Resources Portal > http://www.cisco.com/web/learning/employer_resources/index.html > _______________________________________________ > CDAO-discuss mailing list > CDA...@li... > https://lists.sourceforge.net/lists/listinfo/cdao-discuss ------- Arlin Stoltzfus (ar...@um...) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD, 20850 tel: 240 314 6208; web: www.molevol.org |
From: Hilmar L. <hl...@ne...> - 2013-04-05 22:14:59
|
This is from a post to R-SIG-phylo. What do folks here think about using the following part of the Jmodeltest2 documentation for fleshing out the substitution models section in CDAO? https://code.google.com/p/jmodeltest2/wiki/TheoreticalBackground#Hierarchical_Likelihood_Ratio_Tests_(hLRT) Daniel - while not the kind of answer you were hoping for, I'd be very appreciative if you could forward to me if you do receive pointers to good sources. FYI, CDAO is the Comparative Data Analysis Ontology (http://www.evolutionaryontology.org/). -hilmar On Apr 5, 2013, at 12:23 PM, Daniel Barker wrote: > Hello, > > Is there a review or list of ~every specific nucleotide substitution model > that has been proposed or used in the literature (with references)? > > I'm interested in reversible models. > > The most exhaustive list I have is from the jModeltest documentation, > https://code.google.com/p/jmodeltest2/wiki/TheoreticalBackground#Models_of_ > nucleotide_substitution > > I realise an enormous number of models is possible (and may have been used > in model averaging). I'm keen to know which have some precedent in the > literature, along the lines of those listed above. I'm finding it > difficult to get beyond the standard sources. > > Thank you in advance, > > Daniel > > -- > Daniel Barker > http://bio.st-andrews.ac.uk/staff/db60.htm > The University of St Andrews is a charity registered in Scotland : No > SC013532 > > _______________________________________________ > R-sig-phylo mailing list - R-s...@r-... > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r-s...@r-.../ -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
From: Hilmar L. <hl...@ne...> - 2013-03-13 02:51:52
|
I know it is inevitable, which is why archiving the project stats was on my todo list, just hadn't gotten to that yet. Stats are rather important to have for grant-funded projects, even if their meaning is debatable. So before you do this for any other project, you may want to be sure to archive the stats first (the upgrade clearly states that these will be lost). Or just ask first :-) -hilmar Sent with a tap. On Mar 12, 2013, at 9:40 PM, Jim Balhoff <ba...@ne...> wrote: > Hi Hilmar, > > I confess, it was I! I intended to send an email to this list, but you beat me to it. According to Sourceforge the upgrade is inevitable, so it can be done on request now or instead when they make it mandatory. > > If you have checked out the project via SVN, you will need to checkout again using one of the options listed here: > > https://sourceforge.net/p/cdao/code/15/tree/ > > Thanks, > Jim > > > On Mar 12, 2013, at 5:24 PM, Hilmar Lapp <hl...@ne...> wrote: > >> Did someone request the upgrade of the CDAO repository on SourceForge? It was apparently upgraded today, upon request. >> >> It's not the end of the world by any means, but it does mean that we've just lost all our project stats, and the svn checkout URL changed. I.e., anyone who has a checkout will need to checkout again, as the old one is read-only now. >> >> -hilmar >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >> =========================================================== >> >> >> >> >> ------------------------------------------------------------------------------ >> Everyone hates slow websites. So do we. >> Make your web apps faster with AppDynamics >> Download AppDynamics Lite for free today: >> http://p.sf.net/sfu/appdyn_d2d_mar >> _______________________________________________ >> CDAO-discuss mailing list >> CDA...@li... >> https://lists.sourceforge.net/lists/listinfo/cdao-discuss > > ____________________________________________ > James P. Balhoff, Ph.D. > National Evolutionary Synthesis Center > 2024 West Main St., Suite A200 > Durham, NC 27705 > USA > > > |
From: Jim B. <ba...@ne...> - 2013-03-13 01:40:52
|
Hi Hilmar, I confess, it was I! I intended to send an email to this list, but you beat me to it. According to Sourceforge the upgrade is inevitable, so it can be done on request now or instead when they make it mandatory. If you have checked out the project via SVN, you will need to checkout again using one of the options listed here: https://sourceforge.net/p/cdao/code/15/tree/ Thanks, Jim On Mar 12, 2013, at 5:24 PM, Hilmar Lapp <hl...@ne...> wrote: > Did someone request the upgrade of the CDAO repository on SourceForge? It was apparently upgraded today, upon request. > > It's not the end of the world by any means, but it does mean that we've just lost all our project stats, and the svn checkout URL changed. I.e., anyone who has a checkout will need to checkout again, as the old one is read-only now. > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_mar > _______________________________________________ > CDAO-discuss mailing list > CDA...@li... > https://lists.sourceforge.net/lists/listinfo/cdao-discuss ____________________________________________ James P. Balhoff, Ph.D. National Evolutionary Synthesis Center 2024 West Main St., Suite A200 Durham, NC 27705 USA |
From: Hilmar L. <hl...@ne...> - 2013-03-12 22:47:01
|
Did someone request the upgrade of the CDAO repository on SourceForge? It was apparently upgraded today, upon request. It's not the end of the world by any means, but it does mean that we've just lost all our project stats, and the svn checkout URL changed. I.e., anyone who has a checkout will need to checkout again, as the old one is read-only now. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
From: Jim B. <ba...@ne...> - 2013-02-05 17:28:43
|
Hi Hilmar, I just made a release for you. - Jim On Feb 2, 2013, at 4:28 PM, Hilmar Lapp <hl...@ne...> wrote: > The class cdao:SetOfThings had a property restriction with universal quantification "has_Element only Character". This is a bug because there is a subclass cdao:SetofNodes with obvious conflict (asserted as "has_Element only Node"). I.e., if an instance of the element is asserted, it will be inferred as an instance of both cdao:Node and cdao:Character, which is non-sensical (even if these aren't expressly declared as disjoint). > > I fixed this by deleting the restriction from the SetOfThings class. > > In addition, I also made the subclasses of cdao:CDAOAnnotation consistent in being defined through the appropriate property restrictions. I hope this is uncontroversial. > > There were a series of other issues / proposed improvements coming out of the Phylotastic II hackathon that just ended in Tucson. I'll post those to the tracker one by one, and presumably some or most of these will trigger some discussion. > > However, can we in the meantime do I new release? I've already updated the version number in anticipation of that. > > Jim - can you initiate this, or tell me what I need to do, or is this documented somewhere? > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_jan > _______________________________________________ > CDAO-discuss mailing list > CDA...@li... > https://lists.sourceforge.net/lists/listinfo/cdao-discuss ____________________________________________ James P. Balhoff, Ph.D. National Evolutionary Synthesis Center 2024 West Main St., Suite A200 Durham, NC 27705 USA |
From: Hilmar L. <hl...@ne...> - 2013-02-02 22:28:41
|
The class cdao:SetOfThings had a property restriction with universal quantification "has_Element only Character". This is a bug because there is a subclass cdao:SetofNodes with obvious conflict (asserted as "has_Element only Node"). I.e., if an instance of the element is asserted, it will be inferred as an instance of both cdao:Node and cdao:Character, which is non-sensical (even if these aren't expressly declared as disjoint). I fixed this by deleting the restriction from the SetOfThings class. In addition, I also made the subclasses of cdao:CDAOAnnotation consistent in being defined through the appropriate property restrictions. I hope this is uncontroversial. There were a series of other issues / proposed improvements coming out of the Phylotastic II hackathon that just ended in Tucson. I'll post those to the tracker one by one, and presumably some or most of these will trigger some discussion. However, can we in the meantime do I new release? I've already updated the version number in anticipation of that. Jim - can you initiate this, or tell me what I need to do, or is this documented somewhere? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
From: Arlin S. <ar...@um...> - 2012-06-11 14:26:23
|
Thanks for the update, Jim! Could you explain briefly how CDAO was used at the Phylotastic hackathon? Arlin On Jun 7, 2012, at 12:45 PM, Jim Balhoff wrote: > We have made a new release of CDAO as part of the NESCent Phylotastic hackathon. The ontology now uses an IRI following the OBO convention, and can be retrieved from there: > > http://purl.obolibrary.org/obo/cdao.owl > > All the terms use OBO numeric IDs, with the previous local names moved to RDFS labels. There is a mapping file with equivalence axioms for the old IDs to the new ones available here: > > http://cdao.svn.sourceforge.net/viewvc/cdao/trunk/ontology/cdao-deprecated-mappings.owl > > I will make a PURL for that file also. I need to make some requests of the PURL manager for OBO so that the version-specific ontology IRIs resolve correctly. For example, the version IRI of the current release is: > > http://purl.obolibrary.org/obo/cdao/2012-06-06/cdao.owl > > Thanks, > Jim > > ____________________________________________ > James P. Balhoff, Ph.D. > National Evolutionary Synthesis Center > 2024 West Main St., Suite A200 > Durham, NC 27705 > USA > > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > CDAO-discuss mailing list > CDA...@li... > https://lists.sourceforge.net/lists/listinfo/cdao-discuss ------- Arlin Stoltzfus (ar...@um...) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD tel: 240 314 6208; web: www.molevol.org |
From: Hilmar L. <hl...@ne...> - 2012-06-10 03:02:37
|
I should add that this new version of CDAO also has the extraneous imports of MAO, an amino acid ontology, and an ontology of phylogenetic methods removed. An ontology that imports those along with the "pure" CDAO, and includes the equivalence and subclass axioms is now available as the following: http://cdao.svn.sourceforge.net/viewvc/cdao/trunk/ontology/cdao-ontology-mappings.owl BTW the http://purl.obolibrary.org/obo/cdao.owl seems to be down or corrupt right now - hopefully that will be fixed soon. -hilmar On Jun 7, 2012, at 12:45 PM, Jim Balhoff wrote: > We have made a new release of CDAO as part of the NESCent Phylotastic hackathon. The ontology now uses an IRI following the OBO convention, and can be retrieved from there: > > http://purl.obolibrary.org/obo/cdao.owl > > All the terms use OBO numeric IDs, with the previous local names moved to RDFS labels. There is a mapping file with equivalence axioms for the old IDs to the new ones available here: > > http://cdao.svn.sourceforge.net/viewvc/cdao/trunk/ontology/cdao-deprecated-mappings.owl > > I will make a PURL for that file also. I need to make some requests of the PURL manager for OBO so that the version-specific ontology IRIs resolve correctly. For example, the version IRI of the current release is: > > http://purl.obolibrary.org/obo/cdao/2012-06-06/cdao.owl > > Thanks, > Jim > > ____________________________________________ > James P. Balhoff, Ph.D. > National Evolutionary Synthesis Center > 2024 West Main St., Suite A200 > Durham, NC 27705 > USA > > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > CDAO-discuss mailing list > CDA...@li... > https://lists.sourceforge.net/lists/listinfo/cdao-discuss -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
From: Jim B. <ba...@ne...> - 2012-06-07 16:45:14
|
We have made a new release of CDAO as part of the NESCent Phylotastic hackathon. The ontology now uses an IRI following the OBO convention, and can be retrieved from there: http://purl.obolibrary.org/obo/cdao.owl All the terms use OBO numeric IDs, with the previous local names moved to RDFS labels. There is a mapping file with equivalence axioms for the old IDs to the new ones available here: http://cdao.svn.sourceforge.net/viewvc/cdao/trunk/ontology/cdao-deprecated-mappings.owl I will make a PURL for that file also. I need to make some requests of the PURL manager for OBO so that the version-specific ontology IRIs resolve correctly. For example, the version IRI of the current release is: http://purl.obolibrary.org/obo/cdao/2012-06-06/cdao.owl Thanks, Jim ____________________________________________ James P. Balhoff, Ph.D. National Evolutionary Synthesis Center 2024 West Main St., Suite A200 Durham, NC 27705 USA |
From: Hilmar L. <hl...@ne...> - 2012-03-24 03:05:20
|
I could take that over, though I'd switch to a different registrar that costs significantly less. -hilmar Sent with a tap. On Mar 22, 2012, at 1:54 PM, Arlin Stoltzfus <ar...@um...> wrote: > Dear all-- > > The registration for evolutionaryontology.org will expire in 2 weeks. CDAO is mapped to this domain. I registered it myself with register.com. > > As I'm not leading the CDAO project anymore, I think it would be appropriate to transfer ownership to someone else. It costs a modest fee to register every year ( $35 per year, less if you renew for multiple years). At the very least, someone should be listed in addition to me as an administrator. > > In principle, evolutionaryontology is a slightly broader concept than CDAO, so I have been willing to share the domain with anyone else working on an evolutionary ontology (though it hasn't happened yet). > > Who would like to take over this responsibility? > > Arlin > ------- > Arlin Stoltzfus (ar...@um...) > Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST > IBBR, 9600 Gudelsky Drive, Rockville, MD > tel: 240 314 6208; web: www.molevol.org > > > ------------------------------------------------------------------------------ > This SF email is sponsosred by: > Try Windows Azure free for 90 days Click Here > http://p.sf.net/sfu/sfd2d-msazure > _______________________________________________ > CDAO-discuss mailing list > CDA...@li... > https://lists.sourceforge.net/lists/listinfo/cdao-discuss |
From: Arlin S. <ar...@um...> - 2012-03-22 18:28:58
|
Dear all-- The registration for evolutionaryontology.org will expire in 2 weeks. CDAO is mapped to this domain. I registered it myself with register.com. As I'm not leading the CDAO project anymore, I think it would be appropriate to transfer ownership to someone else. It costs a modest fee to register every year ( $35 per year, less if you renew for multiple years). At the very least, someone should be listed in addition to me as an administrator. In principle, evolutionaryontology is a slightly broader concept than CDAO, so I have been willing to share the domain with anyone else working on an evolutionary ontology (though it hasn't happened yet). Who would like to take over this responsibility? Arlin ------- Arlin Stoltzfus (ar...@um...) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD tel: 240 314 6208; web: www.molevol.org |
From: Arlin S. <ar...@um...> - 2012-02-27 20:50:12
|
I haven't heard of any such interaction. Note that this JSON file format aims to support something broader than just an OTU X character matrix. Arlin On Feb 20, 2012, at 3:40 PM, Vision, Todd J wrote: > I think there's an opportunity here to find common cause with other > active developers interested in interoperability of comparative > observational data. Has there been any interaction with the BIOM > group already? > > Todd > > ******** > > Date: Mon, 20 Feb 2012 12:00:51 -0700 > From: Greg Caporaso <gre...@gm...> > To: dev...@li... > > GSC developers, > > Attached please find a proposal for recognition of the Biological > Observation Matrix (BIOM, pronounced 'biome') format as a GSC Core > Project. A brief description of the motivation for this file format is > below (this is also presented as the abstract in the attached PDF). > You can find additional details on the BIOM format at: > > http://www.qiime.org/svn_documentation/documentation/biom_format.html > > I look forward to feedback on this proposal from the GSC community, > and would be very interested in joining a call at some point soon to > discuss the next steps in moving this toward GSC recognition. > > Thanks! > > Greg Caporaso, on behalf of the Biological Observation Matrix (BIOM) > project team > > > Project Abstract: > A central data type in 'comparative -omics' analyses (e.g., > metagenomes, comparative genomics, marker-gene-based community > surveys, and metabolomics) is a sample by observation matrix. In > marker gene surveys, this would contain counts of OTUs on a per-sample > basis; in metagenome analyses, this might contain counts of > orthologous groups of genes, taxa, or enzymatic activity on a > per-metagenome basis; in comparative genomics, this would contain > counts of genes or orthologous groups on a per-genome basis. Many > tools have been developed to analyze this data, but are generally > focused on a specific type of study (e.g., QIIME for marker gene > analysis; MG-RAST for metagenome analysis; VAMPS for taxonomic > analysis). Many of the techniques, however, generalize across data > types (e.g., rarefaction analysis/collector curves are generally > applicable to all of these data types). A standard format for the > sample by observation matrix will support interoperability of these > tools, and facilitate development of future analysis tools. > Additionally the incorporation of sample and observation metadata in > this file allows for convenient sharing and archiving of these data > within a single file. > > The BIOM file format has been developed with input from the QIIME, > MG-RAST, and VAMPS development groups. BIOM format is based on JSON, a > human?readable, open standard for data exchange. In addition to > consolidating data and metadata in a single standard file format, BIOM > supports sparse and dense matrix representations to efficiently store > these data on disk. Sparse representations of QIIME OTU tables in BIOM > format, for example, can be more than 3X smaller than the same data > represented in tab-delimited text. > > To support the use of this file format a new open-source software > package will be available at http://biom-format.sourceforge.net. This > will include a format validator, and new Python objects to support > working with this data. This software package will additionally serve > as a repository where other developers can submit implementations of > these objects in other languages. Full format and API documentation > (for the Python objects) will be available to coincide with submission > of an article describing the BIOM format (target submission date of > late Feb 2012). Draft documentation is currently available at > http://biom-format.org. > ------------------------------------------------------------------------------ > Try before you buy = See our experts in action! > The most comprehensive online learning library for Microsoft > developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, > MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-dev2 > _______________________________________________ > Nexml-discuss mailing list > Nex...@li... > https://lists.sourceforge.net/lists/listinfo/nexml-discuss ------- Arlin Stoltzfus (ar...@um...) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD tel: 240 314 6208; web: www.molevol.org |
From: Hilmar L. <hl...@ne...> - 2012-02-21 05:29:51
|
Every year, the number and size of available species phylogenies grows, with the largest trees now exceeding 10^5 tips. The information contained in these megatrees is tremendous, but there is no easy way to access and use it. To address this issue, a NESCent working group, named HIP (Hackathons, Interoperability, Phylogenies), has planned a hackathon (http://en.wikipedia.org/wiki/Hackathon) in which scientist-programmers will design and implement Phylotastic!, an open software system to extract a phylogeny for a named set of species from available megatrees, and optionally create mash-ups with data from online services. Phylotastic is envisioned as a set of web services that collectively provides the operations - pruning, grafting, name-reconciliation, branch estimation, translation - that will democratize using the Tree of Life, making it accessible and computable for researchers throughout the life sciences, from community ecology to comparative genomics Applications are now being accepted to participate in the Phylotastic hackathon, which will take place June 4 to 8 at NESCent headquarters in Durham, NC (see below, How to Apply). Support for travel and meal expenses will be available to each successful applicant, according to his or her stated needs. We urge you to apply if you are enthusiastic about the goals of the project, and you have one or more of the following skills: o development, adaptation and use of software for megatree informatics, o grafting & pruning trees, o branch length estimation, o NeXML support, o provenance annotation, o mashups (semantic integration), o taxonomic name resolution, o phylogenetic visualization, o construction of and programming with web service interfaces, and o assembling web-services into executable workflows . We also welcome your application if you can envision a role for yourself based on other attributes not listed, including non-programming skills (e.g., generating documentation) and expert knowledge of use-cases (i.e., real-world problems). To understand how you might be able to contribute, please review a brief slide presentation (ppt format, http://bit.ly/xGvwRr, or PDF format, http://bit.ly/wcQzMI). If further information is needed, consult the Phylotastic project wiki (http://www.evoio.org/wiki/Phylotastic), or contact a member of the HIP leadership team (listed below). Sincerely, Hilmar Lapp(*) hl...@ne... * on behalf of the HIP (Hackathons, Interoperability and Phylogenies) Leaderhip Team 1. HOW TO APPLY You may apply by filling in the online form here: http://tinyurl.com/PhyloTasticForm Please note the following: o The application deadline is March 4 at midnight, EST o Be sure that you understand the project before applying. If needed, review a brief slide presentation (ppt format, http://bit.ly/xGvwRr, or PDF format, http://bit.ly/wcQzMI). o The application form asks you to describe your qualifications. If possible, cite tangible accomplishments to provide evidence of your skills. o All code produced at the event is to be made available immediately under an OSI-approved open-source license, and documentation under a Creative Commons BY license (http://creativecommons.org/licenses/by/3.0/). Using the online application, indicate whether this would pose any difficulty for your participation. Support for travel and meal expenses will be available to each successful applicant, according to his or her stated needs. Please understand that your application is not a guarantee of participation in the event. Funds and space are limited: we may not be able to sponsor every individual who is qualified to participate. 2. SCOPING STATEMENTS To further clarify the project, consider the following points. In scope: o Populating data store of existing trees o Evolution of PhyloWS to support the needs of PhyloTastic o Taxonomic name resolution (embedding existing TNRS capacities) o Pruning trees and grafting species on them o Branch length (existing methods for incorporating branch lengths) o Integration of data and trees (e.g., mashups) - species-wise integration o Display of resulting trees (using existing technologies) o Wrap all these existing tools as web services o NeXML syntax extensions if needed o If needed, determine methods for compressing NeXML representations o user interfaces that are simple (web form) or that adapt existing tools Not In Scope: o Constructing new input trees o New Data Generation o Arguing or evaluating the correctness of trees o Design of new TNRS systems o Debates about which naming system is best o Developing new techniques to derive branch lengths Uncertain: o Phylo-referencing o Satisfying any particular standard of provenance annotation 3. HIP (Hackathons, Interoperability, Phylogenetics) The Phylotastic Hackathon represents the first of three sponsored by a new working group at NESCent called HIP (Hackathons, Interoperability, Phylogenetics). HIP is organized by a Leadership Team consisting of Karen Cranston, Sergei Kosakovsky Pond, Hilmar Lapp, Enrico Pontelli (PI), Michael Rosenberg, Brian Sidlauskas, Arlin Stoltzfus (PI), Rutger Vos (PI), Mark Westneat, and Mark Wilkinson. More information about HIP, including goals, strategies, and project ideas, can be found here: http://www.evoio.org/wiki/HIP -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
From: Vision, T. J <tj...@bi...> - 2012-02-20 21:14:36
|
I think there's an opportunity here to find common cause with other active developers interested in interoperability of comparative observational data. Has there been any interaction with the BIOM group already? Todd ******** Date: Mon, 20 Feb 2012 12:00:51 -0700 From: Greg Caporaso <gre...@gm...> To: dev...@li... GSC developers, Attached please find a proposal for recognition of the Biological Observation Matrix (BIOM, pronounced 'biome') format as a GSC Core Project. A brief description of the motivation for this file format is below (this is also presented as the abstract in the attached PDF). You can find additional details on the BIOM format at: http://www.qiime.org/svn_documentation/documentation/biom_format.html I look forward to feedback on this proposal from the GSC community, and would be very interested in joining a call at some point soon to discuss the next steps in moving this toward GSC recognition. Thanks! Greg Caporaso, on behalf of the Biological Observation Matrix (BIOM) project team Project Abstract: A central data type in 'comparative -omics' analyses (e.g., metagenomes, comparative genomics, marker-gene-based community surveys, and metabolomics) is a sample by observation matrix. In marker gene surveys, this would contain counts of OTUs on a per-sample basis; in metagenome analyses, this might contain counts of orthologous groups of genes, taxa, or enzymatic activity on a per-metagenome basis; in comparative genomics, this would contain counts of genes or orthologous groups on a per-genome basis. Many tools have been developed to analyze this data, but are generally focused on a specific type of study (e.g., QIIME for marker gene analysis; MG-RAST for metagenome analysis; VAMPS for taxonomic analysis). Many of the techniques, however, generalize across data types (e.g., rarefaction analysis/collector curves are generally applicable to all of these data types). A standard format for the sample by observation matrix will support interoperability of these tools, and facilitate development of future analysis tools. Additionally the incorporation of sample and observation metadata in this file allows for convenient sharing and archiving of these data within a single file. The BIOM file format has been developed with input from the QIIME, MG-RAST, and VAMPS development groups. BIOM format is based on JSON, a human?readable, open standard for data exchange. In addition to consolidating data and metadata in a single standard file format, BIOM supports sparse and dense matrix representations to efficiently store these data on disk. Sparse representations of QIIME OTU tables in BIOM format, for example, can be more than 3X smaller than the same data represented in tab-delimited text. To support the use of this file format a new open-source software package will be available at http://biom-format.sourceforge.net. This will include a format validator, and new Python objects to support working with this data. This software package will additionally serve as a repository where other developers can submit implementations of these objects in other languages. Full format and API documentation (for the Python objects) will be available to coincide with submission of an article describing the BIOM format (target submission date of late Feb 2012). Draft documentation is currently available at http://biom-format.org. |
From: Rutger V. <rut...@gm...> - 2012-02-09 15:12:13
|
> > I've known EDAM for quite a while, in fact it came up in CDAO discussions > some time ago. The EBI has been using it to index their microarray and > other databases. > I'd known of it (because it was one of the stars at the biohackathons) but the extent of it was amazing. The EDAM people actually made the effort to make terms for things such as "the NeXML file format", "a TreeBASE identifiers", "a CDAO annotation". Makes you feel that you're not actually working in a complete vacuum :) > On Feb 9, 2012, at 9:46 AM, Karen Cranston wrote: > > > Nice find, Rutger! I didn't know about this. I like the idea of a GSoC > > project, and I think using ISA-tools is the way to go. > > > > NESCent will be announcing this year's request for PhyloSoC ideas > shortly. > > > > On Thu, Feb 9, 2012 at 8:27 AM, Arlin Stoltzfus <ar...@um...> wrote: > >> Is there a GSOC project here? Take the MIAPA checklist: > >> > >> > http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPADraft#Reconciled_draft_checklist > >> > >> plus some kind of ontology-aware forms interface-- can ISA-tools do > this?-- > >> > >> http://isatab.sourceforge.net/ > >> > >> and EDAM, and create a tool that can be used to satisfy a small set of > >> test-cases. The test-cases would be phylogenetic reports (with some > >> associated data files for tree, alignment, etc) that can be rendered as > >> MIAPA reports, which is what we are aiming at here: > >> > >> http://www.evoio.org/wiki/MIAPA/PhyloWays > >> > >> although this needs more work. > >> > >> Arlin > >> > >> On Feb 9, 2012, at 7:55 AM, Rutger Vos wrote: > >> > >> Hi all, > >> > >> just to bring this to your attention: the EDAM ontology is amazingly > >> extensive, including terms for all the file formats we all love, tree > >> annotation (for which the concept has been aligned > >> with http://www.evolutionaryontology.org/cdao.owl#CDAOAnnotation, > terms for > >> reconstruction methods, etc. Maybe you knew all this, but I was quite > amazed > >> to see it: http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=EDAM > >> > >> Rutger > >> -- > >> Dr. Rutger A. Vos > >> Bioinformaticist > >> NCB Naturalis > >> Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the > >> Netherlands > >> Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands > >> http://rutgervos.blogspot.com > >> > >> -- > >> You received this message because you are subscribed to the Google > >> Groups "MIAPA" group. > >> For more options, visit this group at > >> http://groups.google.com/group/miapa-discuss?hl=en > >> > >> > >> ------- > >> Arlin Stoltzfus (ar...@um...) > >> Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST > >> IBBR, 9600 Gudelsky Drive, Rockville, MD > >> tel: 240 314 6208; web: www.molevol.org > >> > >> -- > >> You received this message because you are subscribed to the Google > >> Groups "MIAPA" group. > >> For more options, visit this group at > >> http://groups.google.com/group/miapa-discuss?hl=en > > > > > > > > -- > > ~~~~~~~~~~~~~~~~~~~~~~~ > > kar...@gm... > > ~~~~~~~~~~~~~~~~~~~~~~~ > > > > -- > > You received this message because you are subscribed to the Google > > Groups "MIAPA" group. > > For more options, visit this group at > > http://groups.google.com/group/miapa-discuss?hl=en > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > -- > You received this message because you are subscribed to the Google > Groups "MIAPA" group. > For more options, visit this group at > http://groups.google.com/group/miapa-discuss?hl=en > -- Dr. Rutger A. Vos Bioinformaticist NCB Naturalis Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands http://rutgervos.blogspot.com |
From: Hilmar L. <hl...@ne...> - 2012-02-09 14:58:33
|
Yes indeed, a GSoC project on polishing / customizing an ISA-tools-based annotation tool was one of the follow-up actions that we discussed at the MIAPA workshop at TDWG in October. I've known EDAM for quite a while, in fact it came up in CDAO discussions some time ago. The EBI has been using it to index their microarray and other databases. -hilmar On Feb 9, 2012, at 9:46 AM, Karen Cranston wrote: > Nice find, Rutger! I didn't know about this. I like the idea of a GSoC > project, and I think using ISA-tools is the way to go. > > NESCent will be announcing this year's request for PhyloSoC ideas shortly. > > On Thu, Feb 9, 2012 at 8:27 AM, Arlin Stoltzfus <ar...@um...> wrote: >> Is there a GSOC project here? Take the MIAPA checklist: >> >> http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPADraft#Reconciled_draft_checklist >> >> plus some kind of ontology-aware forms interface-- can ISA-tools do this?-- >> >> http://isatab.sourceforge.net/ >> >> and EDAM, and create a tool that can be used to satisfy a small set of >> test-cases. The test-cases would be phylogenetic reports (with some >> associated data files for tree, alignment, etc) that can be rendered as >> MIAPA reports, which is what we are aiming at here: >> >> http://www.evoio.org/wiki/MIAPA/PhyloWays >> >> although this needs more work. >> >> Arlin >> >> On Feb 9, 2012, at 7:55 AM, Rutger Vos wrote: >> >> Hi all, >> >> just to bring this to your attention: the EDAM ontology is amazingly >> extensive, including terms for all the file formats we all love, tree >> annotation (for which the concept has been aligned >> with http://www.evolutionaryontology.org/cdao.owl#CDAOAnnotation, terms for >> reconstruction methods, etc. Maybe you knew all this, but I was quite amazed >> to see it: http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=EDAM >> >> Rutger >> -- >> Dr. Rutger A. Vos >> Bioinformaticist >> NCB Naturalis >> Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the >> Netherlands >> Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands >> http://rutgervos.blogspot.com >> >> -- >> You received this message because you are subscribed to the Google >> Groups "MIAPA" group. >> For more options, visit this group at >> http://groups.google.com/group/miapa-discuss?hl=en >> >> >> ------- >> Arlin Stoltzfus (ar...@um...) >> Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST >> IBBR, 9600 Gudelsky Drive, Rockville, MD >> tel: 240 314 6208; web: www.molevol.org >> >> -- >> You received this message because you are subscribed to the Google >> Groups "MIAPA" group. >> For more options, visit this group at >> http://groups.google.com/group/miapa-discuss?hl=en > > > > -- > ~~~~~~~~~~~~~~~~~~~~~~~ > kar...@gm... > ~~~~~~~~~~~~~~~~~~~~~~~ > > -- > You received this message because you are subscribed to the Google > Groups "MIAPA" group. > For more options, visit this group at > http://groups.google.com/group/miapa-discuss?hl=en -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
From: Karen C. <kar...@gm...> - 2012-02-09 14:46:40
|
Nice find, Rutger! I didn't know about this. I like the idea of a GSoC project, and I think using ISA-tools is the way to go. NESCent will be announcing this year's request for PhyloSoC ideas shortly. On Thu, Feb 9, 2012 at 8:27 AM, Arlin Stoltzfus <ar...@um...> wrote: > Is there a GSOC project here? Take the MIAPA checklist: > > http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPADraft#Reconciled_draft_checklist > > plus some kind of ontology-aware forms interface-- can ISA-tools do this?-- > > http://isatab.sourceforge.net/ > > and EDAM, and create a tool that can be used to satisfy a small set of > test-cases. The test-cases would be phylogenetic reports (with some > associated data files for tree, alignment, etc) that can be rendered as > MIAPA reports, which is what we are aiming at here: > > http://www.evoio.org/wiki/MIAPA/PhyloWays > > although this needs more work. > > Arlin > > On Feb 9, 2012, at 7:55 AM, Rutger Vos wrote: > > Hi all, > > just to bring this to your attention: the EDAM ontology is amazingly > extensive, including terms for all the file formats we all love, tree > annotation (for which the concept has been aligned > with http://www.evolutionaryontology.org/cdao.owl#CDAOAnnotation, terms for > reconstruction methods, etc. Maybe you knew all this, but I was quite amazed > to see it: http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=EDAM > > Rutger > -- > Dr. Rutger A. Vos > Bioinformaticist > NCB Naturalis > Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the > Netherlands > Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands > http://rutgervos.blogspot.com > > -- > You received this message because you are subscribed to the Google > Groups "MIAPA" group. > For more options, visit this group at > http://groups.google.com/group/miapa-discuss?hl=en > > > ------- > Arlin Stoltzfus (ar...@um...) > Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST > IBBR, 9600 Gudelsky Drive, Rockville, MD > tel: 240 314 6208; web: www.molevol.org > > -- > You received this message because you are subscribed to the Google > Groups "MIAPA" group. > For more options, visit this group at > http://groups.google.com/group/miapa-discuss?hl=en -- ~~~~~~~~~~~~~~~~~~~~~~~ kar...@gm... ~~~~~~~~~~~~~~~~~~~~~~~ |
From: Arlin S. <ar...@um...> - 2012-02-09 13:27:51
|
Is there a GSOC project here? Take the MIAPA checklist: http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPADraft#Reconciled_draft_checklist plus some kind of ontology-aware forms interface-- can ISA-tools do this?-- http://isatab.sourceforge.net/ and EDAM, and create a tool that can be used to satisfy a small set of test-cases. The test-cases would be phylogenetic reports (with some associated data files for tree, alignment, etc) that can be rendered as MIAPA reports, which is what we are aiming at here: http://www.evoio.org/wiki/MIAPA/PhyloWays although this needs more work. Arlin On Feb 9, 2012, at 7:55 AM, Rutger Vos wrote: > Hi all, > > just to bring this to your attention: the EDAM ontology is amazingly extensive, including terms for all the file formats we all love, tree annotation (for which the concept has been aligned with http://www.evolutionaryontology.org/cdao.owl#CDAOAnnotation, terms for reconstruction methods, etc. Maybe you knew all this, but I was quite amazed to see it: http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=EDAM > > Rutger > -- > Dr. Rutger A. Vos > Bioinformaticist > NCB Naturalis > Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands > Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands > http://rutgervos.blogspot.com > > -- > You received this message because you are subscribed to the Google > Groups "MIAPA" group. > For more options, visit this group at > http://groups.google.com/group/miapa-discuss?hl=en ------- Arlin Stoltzfus (ar...@um...) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD tel: 240 314 6208; web: www.molevol.org |