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Re: [Obo-envo] EnvO presentation at the OBO Foundry meeting
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From: Suzanna L. <su...@fr...> - 2009-06-17 21:10:03
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On Jun 17, 2009, at 2:10 PM, Chris Mungall wrote: > > On Jun 17, 2009, at 10:18 AM, Suzanna Lewis wrote: > >> Chris, >> >> What would it take to start creating these links? >> Could we use the cross-product feature in OBO-Edit? > > These would mostly be normal relationships rather than cross- > products. Although there are actually a few classes in GAZ that can > get xp definitions; for example: > > "populated place, Scotland" => def: populated_place THAT located_in > Scotland > > (here we need a class-instance relation for located_in) > > But the majority of IDs in GAZ denote instances rather than classes, > so we mostly want instance_of links between GAZ and ENVO. > > I have a basic transform that will break down a strings such that > "Salton Sea" => instance_of ENVO:sea Could you point us to that (I couldn't find it on the mapping page). Perhaps Michael (or another volunteer) could proof-check these. Likewise, Michael says he might be able to manually add these to the gaz.obo file, through db-xrefs that you could then use to create the links. > > > Trivial but potentially useful, if it can be trusted. Is the Salton > Sea a sea or a lake? Should these classes be disjoint in ENVO? ENVO > currently doesn't give us enough information to make this > distinction (which highlights the importance of getting ENVO used, > rather than remaining an abstract artefact). yes, indeed. > > > In any case, we want to link to more specific classes. For the > Salton Sea we want a class in ENVO like "high-saline content > polluted inland lake". I think this will take a lot of manual > curation effort - but it would be cool to have it. Norman or Dawn, we will need you here to add these as needed. We should start using the tracker for this and I've added this particular term, but there certainly be others. > > > Norman mentioned using terminizer here, but I was a bit suspicious > of some of the links it gave you. See my email on this list on March > 17 "EnvO and Gaz: Tools for linking between terms" > >> Michael, >> If the answer to the above is yes, is this something you might be >> able to work on? > > Let me know if I can help. > > I would probably break this down into two tasks: > > 1) finding very general instance_of links semi-automatically. For > example, we can probably link all the city, country and county > instances to their classes quite trivially. This is good for > ontological completion but less useful for metagenomics data mining > > 2) finding very specific ENVO classes for diverse ranges of GAZ > instances. This will often involve creating new ENVO terms to derive > maximum benefit. Perhaps NLP can help here but I'm not so sure. > > As far as practicalities go, we would probably want to > > a) import ENVO from GAZ > b) Make links between GAZ and ENVO just as you would make normal > relationships > c) set up OE with the correct save filter such that environment > terms get saved in ENVO and places get saved in GAZ > (it gets a bit tricky if the same editor wants to add ENVO terms > and GAZ terms in the same session but I'm guessing Michael will only > do the former) > > Michael's only just making the transition to OE2 and discovering a > few quirks that only transpire when using GAZ so let's give it a bit > of time to sort these out first.. > > another alternative is to manage the inter-ontology links in a > separate bridging file, like what we are doing with the GO external > xps at the moment. > >> >> -S >> >> On Jun 17, 2009, at 11:15 AM, Chris Mungall wrote: >> >>> >>> On Jun 5, 2009, at 11:33 PM, Renzo Kottmann wrote: >>> >>>> Hi Chris, >>>> >>>>>>> 1) What data has been described/annotated using your ontology >>>>>>> (both >>>>>>> type and amount)? >>>>>> In situ environment of isolated prokaryotic cultures which were >>>>>> or are >>>>>> in the process of being sequenced. At the moment 1845 genomes are >>>>>> associated with EnvO terms from the habitat-lite (or whatever the >>>>>> correct name is) subset. >>>>> >>>>> This is fantastic! I think links to this kind of data should be >>>>> displayed prominently on the ENVO page. We are also trying a way >>>>> of >>>>> registering annotated data within the OBO Foundry such that this >>>>> can >>>>> be shown on the OBO ENVO page. >>>> >>>> Thanks. >>>> >>>>> It would be even better if we can deepen these annotations to more >>>>> specific ENVO terms. Would this be a matter of manually >>>>> translating >>>>> some free-text descriptors? >>>> >>>> We plan that Pier Luigi Buttigieg will manually annotate the >>>> genomes in >>>> greater depth in the next weeks. >>> >>> Great! >>> >>>> He will also give a poster presentation >>>> at the M3 SIG meeting at the ISMB in Stockholm. Are you coming? >>> >>> Unfortunately not. >>> >>> I started browsing the data a little more, and have a few >>> questions and suggestions >>> >>> I chose the first sample in a marine habitat with a location: >>> http://www.megx.net/genomes/habitat/marine_habitat.html >>> >>> Acaryochloris sp. CCMEE 5410 Marine habitat located: 33 N 116 W >>> >>> When I click on this location I go to: >>> http://www.megx.net/sites/33,-116.html >>> >>> Which yields the somewhat disappointing: >>> "Interpolated data: The selected location is not in the marine >>> realm. Therefore, no interpolated data is available." >>> >>> I pasted the location into google maps: >>> >>> http://maps.google.com/maps?f=q&source=s_q&hl=en&q=33.000000,+-116.000000&vps=1&jsv=163d&sll=37.0625,-95.677068&sspn=33.764224,93.164063&ie=UTF8&geocode=FUCK9wEdAPsV-Q&split=0 >>> >>> which amusingly puts you right in the middle of the desert!! >>> >>> Switching to google earth and using your nice google map blast >>> tool I realized that this was of course sampled from the Salton Sea. >>> >>> What would be awesome would be a GAZ ID in megx: >>> GAZ:00002462 ! Salton Sea *** [DEF: "An inland saline lake, >>> located in the Colorado Desert in Southern California, north of >>> the Imperial Valley."] >>> >>> It looks like you have the names in your database so it would >>> presumably be possible to do this automatically. >>> >>> So we don't have GAZ-ENVO links yet but when we do I'm sure there >>> will be a lot of useful information for data mining. It seems a >>> shame to tag an organism from such an interesting place with the >>> very general 'marine habitat'. >>> >>> Another point: I would have thought that habitat-lite would >>> contain a subset of ENVO drawn from the 'habitat' hierarchy; but >>> we have: >>> http://www.megx.net/genomes/habitat/water.html >>> >>> which is a type of environmental matter in ENVO. >>> >>> I'm not quite sure what it means to have a habitat of water, and >>> whether marine organisms fall into this subset by default. It >>> appears to be disjoint for organism categorization purposes. >>> >>> All the categories appear to be disjoint. What would you do with, >>> say, an organism-associated marine organism? Would you place it in >>> both categories? Can we assume that anything not in the organism- >>> associated category is free-living? This is perhaps more of a >>> question for ENVO. Some disjointness axioms might help. >>> >>>>> What kinds of analyses are being performed on this data? I think >>>>> it >>>>> would be quite exciting to see what ENVO terms are enriched for >>>>> specific gene sets unique to certain groups of organisms. I'm >>>>> not sure >>>>> this is enough data to drive this kind of analysis, it's a >>>>> useful as a >>>>> demonstration of what ENVO can do >>>> >>>> Pier used the habitat classification to search for marine >>>> specific biased >>>> genes in the genomes during his master thesis and found some >>>> candidates. >>> >>> cool, be interested in seeing that >>> >>>> >>>>>>> 2) How do people query and utilize these data via the ontology? >>>>>> >>>>>> See http://www.megx.net/genomes/genomes.html >>>>> >>>>> * Can the data be downloaded in a tab-delimited format? >>>> >>>> Yes, see http://www.megx.net/genomes/genomes.csv >>> >>> Thanks >>> >>>> >>>> Ciao, >>>> >>>> renzo >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> OpenSolaris 2009.06 is a cutting edge operating system for >>>> enterprises >>>> looking to deploy the next generation of Solaris that includes >>>> the latest >>>> innovations from Sun and the OpenSource community. Download a >>>> copy and >>>> enjoy capabilities such as Networking, Storage and Virtualization. >>>> Go to: http://p.sf.net/sfu/opensolaris-get >>>> _______________________________________________ >>>> Obo-envo mailing list >>>> Obo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/obo-envo >>>> >>> >>> >> >> > > |