November 2005 - tdwg-content

[Tdwg-obs] Survey and Monitoring
by Robert K. Peet 15 Nov '05

15 Nov '05

Hello, Like Lynn, I would like the observations standard to support observations of communities as well as individual organisms Consider the VegBank approach (http://vegbank.org/vegdocs/design/erd/vegbank_erd.pdf): A vegetation plot (location) can have multiple plotObservation events, each of which can have multiple taxonObservation events (collectively such as density, or of individuals), each of which can have multiple identification events, each of which can refer to multiple taxonomic concepts. In addition, the plotObservation can have multiple identifications, and each of these can refer to multiple community concepts. With this approach permanent information about the location, such as geocoordinates, is associated with the plot. Transient information about the plot is recorded with the plotObservation and here we also could refer to protocols applied. Monitoring can be handled by a recursive loop linking plotObservations or taxonObservations Bob Peet ====================================================================== Robert K. Peet, Professor & Chair Phone: 919-962-6942 Curriculum in Ecology, CB#3275 Fax: 919-962-6930 University of North Carolina Cell: 919-368-4971 Chapel Hill, NC 27599-3275 USA Email: peet(a)unc.edu http://www.unc.edu/depts/ecology/ http://www.bio.unc.edu/faculty/peet/ ====================================================================== > Message: 1 > Date: Fri, 11 Nov 2005 15:35:44 -0500 > From: Steve Kelling <stk2(a)cornell.edu> > Subject: [Tdwg-obs] Survey and Monitoring > I apologize for the delay in posting to the listserve. As I am > sure it is true for you, it has been quite hectic for me. > > My feeling is that we have a good definition for the > integrative element of observational data. That is, the element in which > observational data can be (and is) incorporated in existing Natural History > collections data. To reiterate; > An observation is a collection event that describes a phenomenon, and is > bound to the spatiotemporal location where it was made. Furthermore, an > observation describes an occurrence and can be linked to descriptions of > other occurrences. > Now we can begin to talk about the methods of aggregating > observations. To do this means issues such as protocol (including > precision, accuracy, and certainty in the methods), data quality, inferring > negative data, and detectability must be addressed. It is at this point > where observational data can begin to contribute and extend the value of > the data held within biodiversity data networks. > > What I would like to do is begin a discussion on > survey/monitoring techniques and issues. Specifically I would like to > develop the necessary requirements to define methodology metadata. For > example, how does one distinguish between surveys and monitoring? For > example, I consider monitoring as a protocol- driven collection of > observational data gathered repeatedly over a time series at a specific > location. Thus, I would distinguish monitoring from a survey in that a > survey documents an occurrence of an organism(s) at a location at a > particular time, and does not include repeated sampling. > > Anyway, I look forward to hearing from you. > > Regards, > > Steve Kelling > Cornell Lab of Ornithology > 607-254-2478 (work) > 607-342-1029 (cell)

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[Tdwg-obs] Fwd: Re: Survey and Monitoring
by Steve Kelling 13 Nov '05

13 Nov '05

Hello, The definition for the fundamental unit of observational data can certainly include the community concept that Lynn points out. The choice of the term phenomenon, instead of taxon allows for this. I believe that Bob Peet's comments are going to be important in the discussion of aggregating observational data into collecting events (i.e. surveys/monitoring). Vegetation blocks are analogous in bird monitoring to point count transects (the most well known of these in the United States is the Breeding Bird Survey) During a point count transect multiple species (and numbers of individuals) are recorded during each point count during the survey (with BBS there are 50 such point counts). It will be very important that we address how we can organize and/or aggregate point counts or vegetation plot surveys as we incorporate observational data into the general Biodiversity informatics community. "An observation is a collection event that describes a phenomenon, and is bound to the spatiotemporal location where it was made. Furthermore, an observation describes an occurrence and can be linked to descriptions of other occurrences." Regards, Steve >Hi all - Hopefully a quick question / clarification. > >I was wondering if the definition below " ... the element in which >observational data can be (and is) incorporated in existing Natural >History collections data ... " also includes ecological / natural >communities in addition to organisms? There is quite a wealth of >information being collected at this broader more "habitat" level. If >these type of data are implicitly covered, is there a need for clarity >to explicitly state that observations include ecological communities in >addition to organisms? > >Thanks - >Lynn > >At 12:57 PM 11/12/2005 -0500, you wrote: > >>Hello, >> >>Like Lynn, I would like the observations standard to support observations >>of communities as well as individual organisms >> >>Consider the VegBank approach >>(http://vegbank.org/vegdocs/design/erd/vegbank_erd.pdf): >> >>A vegetation plot (location) can have multiple plotObservation events, >>each of which can have multiple taxonObservation events (collectively such >>as density, or of individuals), each of which can have multiple >>identification events, each of which can refer to multiple taxonomic >>concepts. In addition, the plotObservation can have multiple >>identifications, and each of these can refer to multiple community >>concepts. >> >>With this approach permanent information about the location, such as >>geocoordinates, is associated with the plot. Transient information about >>the plot is recorded with the plotObservation and here we also could refer >>to protocols applied. Monitoring can be handled by a recursive loop >>linking plotObservations or taxonObservations >> >>Bob Peet >> ====================================================================== >> Robert K. Peet, Professor & Chair Phone: 919-962-6942 >> Curriculum in Ecology, CB#3275 Fax: 919-962-6930 >> University of North Carolina Cell: 919-368-4971 >> Chapel Hill, NC 27599-3275 USA Email: peet(a)unc.edu >> >> http://www.unc.edu/depts/ecology/ >> http://www.bio.unc.edu/faculty/peet/ >> ====================================================================== >> >> > Message: 1 >> > Date: Fri, 11 Nov 2005 15:35:44 -0500 >> > From: Steve Kelling <stk2(a)cornell.edu> >> > Subject: [Tdwg-obs] Survey and Monitoring >> >> > I apologize for the delay in posting to the listserve. As I am >> > sure it is true for you, it has been quite hectic for me. >> > >> > My feeling is that we have a good definition for the >> > integrative element of observational data. That is, the element in which >> > observational data can be (and is) incorporated in existing Natural >> History >> > collections data. To reiterate; >> > An observation is a collection event that describes a phenomenon, and is >> > bound to the spatiotemporal location where it was made. Furthermore, an >> > observation describes an occurrence and can be linked to descriptions of >> > other occurrences. >> > Now we can begin to talk about the methods of aggregating >> > observations. To do this means issues such as protocol (including >> > precision, accuracy, and certainty in the methods), data quality, >> inferring >> > negative data, and detectability must be addressed. It is at this point >> > where observational data can begin to contribute and extend the value of >> > the data held within biodiversity data networks. >> > >> > What I would like to do is begin a discussion on >> > survey/monitoring techniques and issues. Specifically I would like to >> > develop the necessary requirements to define methodology metadata. For >> > example, how does one distinguish between surveys and monitoring? For >> > example, I consider monitoring as a protocol- driven collection of >> > observational data gathered repeatedly over a time series at a specific >> > location. Thus, I would distinguish monitoring from a survey in that a >> > survey documents an occurrence of an organism(s) at a location at a >> > particular time, and does not include repeated sampling. >> > >> > Anyway, I look forward to hearing from you. >> > >> > Regards, >> > >> > Steve Kelling >> > Cornell Lab of Ornithology >> > 607-254-2478 (work) >> > 607-342-1029 (cell) >> >>_______________________________________________ >>Tdwg-obs mailing list >>Tdwg-obs(a)lists.tdwg.org >>http://lists.tdwg.org/mailman/listinfo/tdwg-obs_lists.tdwg.org > >Steve Kelling >Cornell Lab of Ornithology >607-254-2478 (work) >607-342-1029 (cell) > > Steve Kelling Cornell Lab of Ornithology 607-254-2478 (work) 607-342-1029 (cell)

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Re: [Tdwg-obs] Survey and Monitoring
by Lynn Kutner 11 Nov '05

11 Nov '05

Hi all - Hopefully a quick question / clarification. I was wondering if the definition below " ... the element in which observational data can be (and is) incorporated in existing Natural History collections data ... " also includes ecological / natural communities in addition to organisms? There is quite a wealth of information being collected at this broader more "habitat" level. If these type of data are implicitly covered, is there a need for clarity to explicitly state that observations include ecological communities in addition to organisms? Thanks - Lynn Lynn Kutner NatureServe Email: lynn_kutner(a)natureserve.org Phone: (303) 541-0360 www.natureserve.org -----Original Message----- From: Tdwg-obs-bounces(a)lists.tdwg.org [mailto:Tdwg-obs-bounces@lists.tdwg.org] On Behalf Of Steve Kelling Sent: Friday, November 11, 2005 1:36 PM To: Tdwg-obs(a)lists.tdwg.org Subject: [Tdwg-obs] Survey and Monitoring Greetings, I apologize for the delay in posting to the listserve. As I am sure it is true for you, it has been quite hectic for me. My feeling is that we have a good definition for the integrative element of observational data. That is, the element in which observational data can be (and is) incorporated in existing Natural History collections data. To reiterate; An observation is a collection event that describes a phenomenon, and is bound to the spatiotemporal location where it was made. Furthermore, an observation describes an occurrence and can be linked to descriptions of other occurrences.

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[Tdwg-obs] Survey and Monitoring
by Steve Kelling 11 Nov '05

11 Nov '05

Greetings, I apologize for the delay in posting to the listserve. As I am sure it is true for you, it has been quite hectic for me. My feeling is that we have a good definition for the integrative element of observational data. That is, the element in which observational data can be (and is) incorporated in existing Natural History collections data. To reiterate; An observation is a collection event that describes a phenomenon, and is bound to the spatiotemporal location where it was made. Furthermore, an observation describes an occurrence and can be linked to descriptions of other occurrences. Now we can begin to talk about the methods of aggregating observations. To do this means issues such as protocol (including precision, accuracy, and certainty in the methods), data quality, inferring negative data, and detectability must be addressed. It is at this point where observational data can begin to contribute and extend the value of the data held within biodiversity data networks. What I would like to do is begin a discussion on survey/monitoring techniques and issues. Specifically I would like to develop the necessary requirements to define methodology metadata. For example, how does one distinguish between surveys and monitoring? For example, I consider monitoring as a protocol- driven collection of observational data gathered repeatedly over a time series at a specific location. Thus, I would distinguish monitoring from a survey in that a survey documents an occurrence of an organism(s) at a location at a particular time, and does not include repeated sampling. Anyway, I look forward to hearing from you. Regards, Steve Kelling Cornell Lab of Ornithology 607-254-2478 (work) 607-342-1029 (cell)

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Re: iSpecies
by Roderic Page 02 Nov '05

02 Nov '05

Dear Julian, I've put some quick notes up here: http://darwin.zoology.gla.ac.uk/~rpage/ispecies/how.html. Ideally, if a source provides XML (or something similarly easy to handle, it can be added). As part of other projects I've been playing with getting specimen data from DiGIR providers, for example. Regards Rod NCBI search us On 2 Nov 2005, at 16:48, Julian H wrote: > At 10:33 AM 11/2/2005, you wrote: >> For fun I've created a site that searches three data sources - NCBI, >> Yahoo images, and Google Scholar for information on a taxonomic name. >> If you type in a name you get information on whether that organism has >> been sequenced (and if so, how many sequences are available), the >> first >> five images Yahoo finds on the web, and up to 10 documents from Google >> Scholar (with DOIs and links to PubMed, where available ). >> >> If you'd like to try it go to http://ispecies.org (you'll get >> forwarded >> to a machine here in Glasgow). > > Very cool. Do you have a page on "how it works"? What would be > needed to add another source? > > Keep up the good work, Julian > > > > > > Julian Humphries > DigiMorph.Org > Geological Sciences > University of Texas at Austin > Austin, TX 78712 > 512-471-3275 > > Professor Roderic D. M. Page Editor, Systematic Biology DEEB, IBLS Graham Kerr Building University of Glasgow Glasgow G12 8QP United Kingdom Phone: +44 141 330 4778 Fax: +44 141 330 2792 email: r.page(a)bio.gla.ac.uk web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html Subscribe to Systematic Biology through the Society of Systematic Biologists Website: http://systematicbiology.org Search for taxon names at http://darwin.zoology.gla.ac.uk/~rpage/portal/

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Re: iSpecies
by Martin Grube 02 Nov '05

02 Nov '05

Dear Rod, this is fantastic! Thank you for this great service to science.. an absolutely needed tool ! Cheers, Martin Grube (lichenologist) Roderic Page schrieb: > For fun I've created a site that searches three data sources - NCBI, > Yahoo images, and Google Scholar for information on a taxonomic name. > If you type in a name you get information on whether that organism has > been sequenced (and if so, how many sequences are available), the first > five images Yahoo finds on the web, and up to 10 documents from Google > Scholar (with DOIs and links to PubMed, where available ). > > If you'd like to try it go to http://ispecies.org (you'll get forwarded > to a machine here in Glasgow). > > I know there are all sorts of problems with searching on names, but > I've found it to be fun to see just how much information is out there. > > Example links to try are: > > http://darwin.zoology.gla.ac.uk/~rpage/ispecies/?q=Pediculus+humanus > http://darwin.zoology.gla.ac.uk/~rpage/ispecies/?q=Rhea+americana > http://darwin.zoology.gla.ac.uk/~rpage/ispecies/?q=Anthonomus+grandis > http://darwin.zoology.gla.ac.uk/~rpage/ispecies/? > q=Florinemestrius+pulcherrimus > http://darwin.zoology.gla.ac.uk/~rpage/ispecies/?q=Agathis+australis > http://darwin.zoology.gla.ac.uk/~rpage/ispecies/?q=Banksia+coccinea > > Please be aware that the image search can sometime produce images you > might not want children or the faint hearted to see -- despite Yahoo > claiming it filters adult content. You have been warned... > > Comments welcome. > > Regards > > Rod > > Professor Roderic D. M. Page > Editor, Systematic Biology > DEEB, IBLS > Graham Kerr Building > University of Glasgow > Glasgow G12 8QP > United Kingdom > > Phone: +44 141 330 4778 > Fax: +44 141 330 2792 > email: r.page(a)bio.gla.ac.uk > web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html > reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html > > Subscribe to Systematic Biology through the Society of Systematic > Biologists Website: http://systematicbiology.org > Search for taxon names at http://darwin.zoology.gla.ac.uk/~rpage/portal/ -- Dr. Martin Grube Institute of Plant Sciences Karl-Franzens-Universität Graz Holteigasse 6 8010 Graz Austria tel 0043 316 380 5655 fax 0043 316 380 9883 email martin.grube(a)uni-graz.at

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iSpecies
by Roderic Page 02 Nov '05

02 Nov '05

For fun I've created a site that searches three data sources - NCBI, Yahoo images, and Google Scholar for information on a taxonomic name. If you type in a name you get information on whether that organism has been sequenced (and if so, how many sequences are available), the first five images Yahoo finds on the web, and up to 10 documents from Google Scholar (with DOIs and links to PubMed, where available ). If you'd like to try it go to http://ispecies.org (you'll get forwarded to a machine here in Glasgow). I know there are all sorts of problems with searching on names, but I've found it to be fun to see just how much information is out there. Example links to try are: http://darwin.zoology.gla.ac.uk/~rpage/ispecies/?q=Pediculus+humanus http://darwin.zoology.gla.ac.uk/~rpage/ispecies/?q=Rhea+americana http://darwin.zoology.gla.ac.uk/~rpage/ispecies/?q=Anthonomus+grandis http://darwin.zoology.gla.ac.uk/~rpage/ispecies/? q=Florinemestrius+pulcherrimus http://darwin.zoology.gla.ac.uk/~rpage/ispecies/?q=Agathis+australis http://darwin.zoology.gla.ac.uk/~rpage/ispecies/?q=Banksia+coccinea Please be aware that the image search can sometime produce images you might not want children or the faint hearted to see -- despite Yahoo claiming it filters adult content. You have been warned... Comments welcome. Regards Rod Professor Roderic D. M. Page Editor, Systematic Biology DEEB, IBLS Graham Kerr Building University of Glasgow Glasgow G12 8QP United Kingdom Phone: +44 141 330 4778 Fax: +44 141 330 2792 email: r.page(a)bio.gla.ac.uk web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html Subscribe to Systematic Biology through the Society of Systematic Biologists Website: http://systematicbiology.org Search for taxon names at http://darwin.zoology.gla.ac.uk/~rpage/portal/

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TDWG-2005 SpeciesPages interest group
by Wouter Addink 02 Nov '05

02 Nov '05

At the TDWG meeting in St. Petersburg the SpeciesPages interest group was formed. This group will discuss the needs to exchange SpeciesPage data and might become a formal TDWG subgroup in the future. I've created a WIKI for the SpeciesPages interest group, which can be found at: http://ip50.eti.uva.nl/TDWGSpecies. The Purposes of this WIKI are to gather information about developments and projects which involve SpeciesPages and to discuss the needs to exchange SpeciesPage data. You are invited to use it and to contribute to this WIKI. Registration is not necessary, except if you want to add files. If you know other people that are interested in SpeciesPages, please inform them about this WIKI! Regards, Wouter Addink ETI BioInformatics

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Re: iSpecies
by Julian H 02 Nov '05

02 Nov '05

At 10:33 AM 11/2/2005, you wrote: >For fun I've created a site that searches three data sources - NCBI, >Yahoo images, and Google Scholar for information on a taxonomic name. >If you type in a name you get information on whether that organism has >been sequenced (and if so, how many sequences are available), the first >five images Yahoo finds on the web, and up to 10 documents from Google >Scholar (with DOIs and links to PubMed, where available ). > >If you'd like to try it go to http://ispecies.org (you'll get forwarded >to a machine here in Glasgow). Very cool. Do you have a page on "how it works"? What would be needed to add another source? Keep up the good work, Julian Julian Humphries DigiMorph.Org Geological Sciences University of Texas at Austin Austin, TX 78712 512-471-3275

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