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[Tdwg-obs] more on observation standards
by Jerry Cooper 20 Oct '05

20 Oct '05

Hi all, I'm enclosing an email that Flip Dibner sent me during the TDWG meeting on the OGC effort in the area of 'observations and measurements'. Follow the links below to the documentation. I think they have come up a well though out generalized model that encompasses most of the scenarios I can think of. Perhaps the only down side is the work necessary to pack/unpack data into this form, i.e. as a data exchange standard it looks great, but as an easily understandable working tool it looks heavy. Jerry *------------------------------------------------- Jerry, You can download OGC's O&M Recommendation from their Recommendation Papers page at http://www.opengeospatial.org/specs/?page=recommendation . The direct download link is http://portal.opengeospatial.org/files/?artifact_id=1324 . I would draw your attention in particular to Appendix C.5., Ecological Survey. There is more recent information that I think will accommodate even more of our needs, but I don't have as well organized, and the newest bits are not yet public. I will pull all this together for the sake of the group at large, as suggested by Stan. Flip Phillip C. Dibner Ecosystem Associates (650) 948-3537 (650) 948-7895 Fax ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ WARNING: This email and any attachments may be confidential and/or privileged. They are intended for the addressee only and are not to be read, used, copied or disseminated by anyone receiving them in error. If you are not the intended recipient, please notify the sender by return email and delete this message and any attachments. The views expressed in this email are those of the sender and do not necessarily reflect the official views of Landcare Research. Landcare Research http://www.landcareresearch.co.nz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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[Tdwg-obs] What is an observation?
by Steve Kelling 20 Oct '05

20 Oct '05

Hello, I had several people respond to my query about what kinds of things we should discuss in this list. Overwhelmingly, the interest seemed focused on defining some of the key terms that we are bantering about. To that end I'd like to initiate the first discussion on this list by asking, what is an observation? What follows is some information that I gleaned from the Internet, discussions that I have had with others, and with the ENBI reports. I'd appreciate your comments, in our goal to create a good definintion of observation for our purposes.--Steve Princeton University's Wordnet (<http://wordnet.princeton.edu/>http://wordnet.princeton.edu/) defines an observation as the act of making and then recording a measurement. Basically, something is watched, and notes are taken about it. In the study of biology and astronomy careful observations made by trained observations and amateurs alike, is the foundation of information gathered for these disciplines. With regard to biodiversity informatics, particularly as to how observations relate to the existing infrastructure, the above definition is too general, because it encompasses all facets of biology. Consequently, we need to begin to qualify the definition of observation. First, we restrict our definition to only those observations made of organisms in the environment. Second, the location at which the observation was made is an integral component of the observation. Third, an observation is exclusive of museum voucher specimens. Finally, information collected during an observation includes additional attributes such as: protocol, measure of abundance, extent of occurrence, demographic, ecological associates, and environmental conditions. To discuss and ultimately added to the definition: Advantages of observational data. Disadvantages of observational data Observational data providers (amateurs/professionals) Detectability and data quality Location specificity Integration of observational data Definition of a collecting event and its significance others? Steve Kelling Cornell Lab of Ornithology 607-254-2478 (work) 607-342-1029 (cell)

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[Tdwg-obs] FW: What is an observation?
by Donald Hobern 19 Oct '05

19 Oct '05

I fully agree with Jerry. It may be helpful for us to start not by thinking of observations by themselves, but rather to think of 'surveys' or some other similar higher class of objects. A 'survey' is a definition of the protocols surrounding a set of 'observations' and is the correct place to record all of the information about the methods involved, wherever that falls along Jerry's hypothetical continuum. Each 'observation' is then associated with a 'survey'. The most casual kind of 'observations' may be associated with a null 'survey' indicating that little or nothing can be inferred about the communities, populations and interactions of this and other taxa in the given area on the basis of this isolated point event. It is likely too that 'surveys' need the option of being defined recursively to reflect the fact that a particular 'survey' may itself fit into a higher-level organisation of coordinated activity. For example a transect may be part of an annual series for a given locality, within a national scheme for monitoring a randomly selected set of transects. The main point is that the interest in 'observations' is not exactly the same as for specimens. At an early stage in the development of GBIF, we tended to treat observations as little more than voucherless specimens. This ignores what is generally the most significant aspect of such data, the organisation of those point events into a framework of observations in which every observation (including every zero count) gives context to the others. We need to focus on capturing this, rather than treating 'observation' data simply as a set of modifier attributes to a standard Darwin Core taxon occurrence record. Donald --------------------------------------------------------------- Donald Hobern (dhobern(a)gbif.org) Programme Officer for Data Access and Database Interoperability Global Biodiversity Information Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, Denmark Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 --------------------------------------------------------------- -----Original Message----- From: Tdwg-obs-bounces(a)lists.tdwg.org [mailto:Tdwg-obs-bounces@lists.tdwg.org] On Behalf Of Jerry Cooper Sent: 19 October 2005 23:45 To: Tdwg-obs(a)lists.tdwg.org Subject: Re: [Tdwg-obs] What is an observation? I support Hannu's view. I still see a bit of confusion created by the overlap between 'a natural history oriented observations' and 'survey/monitoring observations'. The former is generally a serendipitous event and is well described within ABCD. The latter generally places a much greater emphasis on recording the relationships between organisms and with the surrounding environment and the methodology used to capture these data. Does the community see a difference between these two - or a continuum between them? Is this group primarily concerned with the former, or the latter, or both? If it is the former then I think I'm in the wrong group, and maybe we need a seprate group to consider survey/monitoring events. If it is the latter, or a continuum, then I restate what I said in St Petersburgh. For survey/monitoring data it is the methodology metdata that takes precedence and that should act as a container for 1 to many observations of organisms and environmental variables. That is the inverse of say, Darwin Core, where an observation on a single organism takes precedence. Hence the difficulty in recording 'absence' data within a Darwin Core-like schema. Jerry Jerry Cooper PhD Research Leader: Biodiversity Informatics Landcare Research PO Box 40, Lincoln 8152 New Zealand +64 3 325 6701 ext 3734 CooperJ(a)LandcareResearch.CO.NZ >>> Hannu Saarenmaa <hsaarenmaa(a)gbif.org> 20/10/2005 3:40 a.m. >>> How about this: An observation captures data about the occurrence of an organism in space and time and in relation to habitat and other organisms. Documenting the precision, accuracy, certainty, and methods of the measurements that have been made during an observation is essential for determining the fitness for use of the data that has been captured. An observation is an event that can be linked to other events. Indeed, I would like to emphasise the need of documenting what is called "quality". Hannu Steve Kelling wrote: >Hello, > >I had several people respond to my query about what kinds of things we >should discuss in this list. Overwhelmingly, the interest seemed focused on >defining some of the key terms that we are bantering about. To that end I'd >like to initiate the first discussion on this list by asking, what is an >observation? > What follows is some information that I gleaned from the Internet, >discussions that I have had with others, and with the ENBI reports. I'd >appreciate your comments, in our goal to create a good definintion of >observation for our purposes.--Steve > >Princeton University's Wordnet >(<http://wordnet.princeton.edu/>http://wordnet.princeton.edu/) defines an >observation as the act of making and then recording a measurement. >Basically, something is watched, and notes are taken about it. In the study >of biology and astronomy careful observations made by trained observations >and amateurs alike, is the foundation of information gathered for these >disciplines. > > >With regard to biodiversity informatics, particularly as to how >observations relate to the existing infrastructure, the above definition is >too general, because it encompasses all facets of biology. Consequently, we >need to begin to qualify the definition of observation. First, we restrict >our definition to only those observations made of organisms in the >environment. Second, the location at which the observation was made is an >integral component of the observation. Third, an observation is exclusive >of museum voucher specimens. Finally, information collected during an >observation includes additional attributes such as: protocol, measure of >abundance, extent of occurrence, demographic, ecological associates, and >environmental conditions. > > To discuss and ultimately added to the definition: > >Advantages of observational data. >Disadvantages of observational data >Observational data providers (amateurs/professionals) >Detectability and data quality >Location specificity >Integration of observational data >Definition of a collecting event and its significance >others? > > >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 > > > -- Hannu Saarenmaa Deputy Director for Informatics Global Biodiversity Information Facility - GBIF Secretariat Universitetsparken 15, DK-2100 Copenhagen Tel +45-35321479 Fax +45-35321480 GSM +45-28751479 hsaarenmaa(a)gbif.org http://www.gbif.org/ _______________________________________________ Tdwg-obs mailing list Tdwg-obs(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-obs_lists.tdwg.org ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ WARNING: This email and any attachments may be confidential and/or privileged. They are intended for the addressee only and are not to be read, used, copied or disseminated by anyone receiving them in error. If you are not the intended recipient, please notify the sender by return email and delete this message and any attachments. The views expressed in this email are those of the sender and do not necessarily reflect the official views of Landcare Research. Landcare Research http://www.landcareresearch.co.nz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ Tdwg-obs mailing list Tdwg-obs(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-obs_lists.tdwg.org

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Re: [Tdwg-obs] What is an observation?
by Jerry Cooper 19 Oct '05

19 Oct '05

I support Hannu's view. I still see a bit of confusion created by the overlap between 'a natural history oriented observations' and 'survey/monitoring observations'. The former is generally a serendipitous event and is well described within ABCD. The latter generally places a much greater emphasis on recording the relationships between organisms and with the surrounding environment and the methodology used to capture these data. Does the community see a difference between these two - or a continuum between them? Is this group primarily concerned with the former, or the latter, or both? If it is the former then I think I'm in the wrong group, and maybe we need a seprate group to consider survey/monitoring events. If it is the latter, or a continuum, then I restate what I said in St Petersburgh. For survey/monitoring data it is the methodology metdata that takes precedence and that should act as a container for 1 to many observations of organisms and environmental variables. That is the inverse of say, Darwin Core, where an observation on a single organism takes precedence. Hence the difficulty in recording 'absence' data within a Darwin Core-like schema. Jerry Jerry Cooper PhD Research Leader: Biodiversity Informatics Landcare Research PO Box 40, Lincoln 8152 New Zealand +64 3 325 6701 ext 3734 CooperJ(a)LandcareResearch.CO.NZ >>> Hannu Saarenmaa <hsaarenmaa(a)gbif.org> 20/10/2005 3:40 a.m. >>> How about this: An observation captures data about the occurrence of an organism in space and time and in relation to habitat and other organisms. Documenting the precision, accuracy, certainty, and methods of the measurements that have been made during an observation is essential for determining the fitness for use of the data that has been captured. An observation is an event that can be linked to other events. Indeed, I would like to emphasise the need of documenting what is called "quality". Hannu Steve Kelling wrote: >Hello, > >I had several people respond to my query about what kinds of things we >should discuss in this list. Overwhelmingly, the interest seemed focused on >defining some of the key terms that we are bantering about. To that end I'd >like to initiate the first discussion on this list by asking, what is an >observation? > What follows is some information that I gleaned from the Internet, >discussions that I have had with others, and with the ENBI reports. I'd >appreciate your comments, in our goal to create a good definintion of >observation for our purposes.--Steve > >Princeton University's Wordnet >(<http://wordnet.princeton.edu/>http://wordnet.princeton.edu/) defines an >observation as the act of making and then recording a measurement. >Basically, something is watched, and notes are taken about it. In the study >of biology and astronomy careful observations made by trained observations >and amateurs alike, is the foundation of information gathered for these >disciplines. > > >With regard to biodiversity informatics, particularly as to how >observations relate to the existing infrastructure, the above definition is >too general, because it encompasses all facets of biology. Consequently, we >need to begin to qualify the definition of observation. First, we restrict >our definition to only those observations made of organisms in the >environment. Second, the location at which the observation was made is an >integral component of the observation. Third, an observation is exclusive >of museum voucher specimens. Finally, information collected during an >observation includes additional attributes such as: protocol, measure of >abundance, extent of occurrence, demographic, ecological associates, and >environmental conditions. > > To discuss and ultimately added to the definition: > >Advantages of observational data. >Disadvantages of observational data >Observational data providers (amateurs/professionals) >Detectability and data quality >Location specificity >Integration of observational data >Definition of a collecting event and its significance >others? > > >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 > > > -- Hannu Saarenmaa Deputy Director for Informatics Global Biodiversity Information Facility - GBIF Secretariat Universitetsparken 15, DK-2100 Copenhagen Tel +45-35321479 Fax +45-35321480 GSM +45-28751479 hsaarenmaa(a)gbif.org http://www.gbif.org/ _______________________________________________ Tdwg-obs mailing list Tdwg-obs(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-obs_lists.tdwg.org ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ WARNING: This email and any attachments may be confidential and/or privileged. They are intended for the addressee only and are not to be read, used, copied or disseminated by anyone receiving them in error. If you are not the intended recipient, please notify the sender by return email and delete this message and any attachments. The views expressed in this email are those of the sender and do not necessarily reflect the official views of Landcare Research. Landcare Research http://www.landcareresearch.co.nz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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Re: TDWG Image Interest Group
by Rob Stevenson 19 Oct '05

19 Oct '05

I am very glad to hear this is happening. Rob Bob Morris wrote: > At the recent St. Petersburg meeting of the Taxonomic Databases Working > Group, I convened the Image Interest Group. Preliminary to forming a > formal TDWG subgroup, the Image Interest Group will discuss what should > be the concerns for biodiversity multimedia standards especially as they > relate to other TDWG standards, where can one find resources about > biodiversity, and other, image acquisition and management, and what > should be the charter of a full subgroup. > > Most such discussion should take place on the TDWGImage wiki > http://wiki.cs.umb.edu/twiki/bin/view/TDWGImage, where you are invited > to peruse, comment, register, set an RSS feed or all of the above. You > need to register only if you want to comment or want mail notice of > discussion. (RSS is better!). In addition, you can join a mail > discussion list Tdwg-image(a)lists.tdwg.org, but the wiki is the preferred > discussion locus. The mailing list will automatically receive notices of > posting in the wiki and will mainly be the focus of transient messages > about topics of interest. To subscribe to the mailing list, visit > http://lists.tdwg.org/mailman/listinfo/tdwg-img_lists.tdwg.org > > Please feel free to send this message to other lists or colleagues you > think might find it valuable. > > Bob Morris > UMASS-Boston Electronic Field Guide Project > http://efg.cs.umb.edu > > -- > Robert A. Morris > Professor of Computer Science > UMASS-Boston > http://www.cs.umb.edu/~ram > phone (+1)617 287 6466 -- R.D. Stevenson Dept. of Biology UMass Boston MA 02125-3393 tel 617-287-6572 fax 617-287-6650 http://www.cs.umb.edu/efg/

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TDWG Image Interest Group
by Bob Morris 17 Oct '05

17 Oct '05

At the recent St. Petersburg meeting of the Taxonomic Databases Working Group, I convened the Image Interest Group. Preliminary to forming a formal TDWG subgroup, the Image Interest Group will discuss what should be the concerns for biodiversity multimedia standards especially as they relate to other TDWG standards, where can one find resources about biodiversity, and other, image acquisition and management, and what should be the charter of a full subgroup. Most such discussion should take place on the TDWGImage wiki http://wiki.cs.umb.edu/twiki/bin/view/TDWGImage, where you are invited to peruse, comment, register, set an RSS feed or all of the above. You need to register only if you want to comment or want mail notice of discussion. (RSS is better!). In addition, you can join a mail discussion list Tdwg-image(a)lists.tdwg.org, but the wiki is the preferred discussion locus. The mailing list will automatically receive notices of posting in the wiki and will mainly be the focus of transient messages about topics of interest. To subscribe to the mailing list, visit http://lists.tdwg.org/mailman/listinfo/tdwg-img_lists.tdwg.org Please feel free to send this message to other lists or colleagues you think might find it valuable. Bob Morris UMASS-Boston Electronic Field Guide Project http://efg.cs.umb.edu -- Robert A. Morris Professor of Computer Science UMASS-Boston http://www.cs.umb.edu/~ram phone (+1)617 287 6466

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ABCD 2.0
by Camiel Dijkers 28 Apr '05

28 Apr '05

Hi all. I'm looking for a sample xml-file in ABCD 2.0 format, containing some taxonomical data. It doesn't have to be large, but should contain some data I can visually check for consistancy. I apologise if this isn't the correct forum to make this request, but it was all I could find. Can someone help me to get such a file, or direct me to the correct place to ask for this? Thanks for your time. Camiel Dijkers | Please read our E-mail Disclaimer at http://www.grontmij.com/emaildisclaimer |

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Key to the Pseudosaurs of the Natural History Museums of the World
by Bob Morris 27 Apr '05

27 Apr '05

A key to the Pseudosaurs of the Natural History Museums of the World has been released, with initial emphasis on specimens held by the Smithsonian Institution National Museum of Natural History. Please see http://aardvark.cs.umb.edu:8080/keys We welcome commentary and learned discussion at http://wiki.cs.umb.edu/twiki/bin/view/BDEI/Pseudosaurs Bob Morris -- Robert A. Morris Professor of Computer Science UMASS-Boston ram(a)cs.umb.edu http://www.cs.umb.edu/efg http://www.cs.umb.edu/~ram phone (+1)617 287 6466

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SDD 1.0 beta 4
by Gregor Hagedorn 19 Mar '05

19 Mar '05

I have uploaded a new version of the SDD schema that is accessible from: http://wiki.cs.umb.edu/twiki/bin/view/SDD/CurrentSchemaVersion This upload is in accordance with the regulations of TDWG which require a final draft 180 days prior to the voting session (at TDWG 2005, St. Petersburg). I very urgently look forward to criticism. However at the moment only schema- wise people with a schema viewer are able to do this. Those of you looking for example files and generated html schema documentation - please bear with me a little longer, these items are not yet finished. All the best Gregor---------------------------------------------------------- Gregor Hagedorn (G.Hagedorn(a)bba.de) Institute for Plant Virology, Microbiology, and Biosafety Federal Research Center for Agriculture and Forestry (BBA) Königin-Luise-Str. 19 Tel: +49-30-8304-2220 14195 Berlin, Germany Fax: +49-30-8304-2203

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LSID protocol handler for Mozilla/Firefox - oops
by Roderic D. M. Page 13 Dec '04

13 Dec '04

Of course, it would have helped if I'd included the address of the web site where the LSID protocol handler is available (duh!). The address is http://darwin.zoology.gla.ac.uk/~rpage/lsid/ . Regards Rod -- -------------------------------------------------------- Professor Roderic D. M. Page Editor Elect, 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

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