February 2006 - tdwg-content

[Tdwg-img] TDWG Technical Architecture Group Meeting Call
by Roger Hyam 10 Feb '06

10 Feb '06

Dear Imaging List Member, As you may be aware the GUID-1 meeting has now taken place. The outcome of this meeting has wide ranging repercussions for all TDWG standards and their future interoperability. I am therefore calling a Technical Architecture Group meeting as soon as possible to discuss the best way to proceed. This meeting will be able to discuss issues, such as shared vocabularies, which are outside the scope of the GUID project. You can read more about the proposed meeting here: http://www.tdwg.hyam.net/twiki/bin/view/TAG/TagMeeting1 I would be grateful if you would consider whether you might attend or nominate some one to attend. If you would like to discuss the meeting further please join the TAG list to save generating traffic on this list (http://www.tdwg.org/mailinglists.htm) Best wishes, Roger (apologies if you have received this multiple times as it is going to several TDWG lists). -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org roger(a)tdwg.org +44 1578 722782 -------------------------------------

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[Tdwg-obs] Antw: Re: On observation definition / moving forward
by SABINE ROSCHER 10 Feb '06

10 Feb '06

Hello, We work in the field of agrobiodiversity, e.g. crop wild relatives. For us the combination of oberservation data and samples is very important. We consider the unit as central element, which can be a part of an organism, an ogranism, or a group of organisms. The reason for going under the level of organism is that sometimes the plant with all roots etc. can be quite larger than the part that is observed and recorded for a certain location. This describes the line we think along : "A unit in our context is uniquely identified by time, place(site) and taxonomy. In addition a particular unit could be sampled to further assist in characterising it. Such samples could be (1) seed samples/planting material (classical ex situ accessions), (2) photos or (3) herbarium vouchers." UNIT {time, site, taxonomy} (+ sample) (With regard to the prior discussion I agree that we also have to handle legacy data with missing entries for time and place.) Sabine Sabine Roscher 513 - Informations- und Koordinationszentrum für Biologische Vielfalt (IBV) Bundesanstalt für Landwirtschaft und Ernährung Deichmanns Aue 29, 53179 Bonn Tel.: +49 (0)228 6845-3235 (oder -3237) Fax: +49 (0)228 6845-3787 E-Mail: sabine.roscher(a)ble.de Internet: www.ble.de weiterführende Information: www.genres.de >>> Steve Kelling <stk2(a)cornell.edu> 09.02.2006 18:55 >>> Hello, I really like the improvements made on the definition, and I might suggest that I put it up on the TDWG-obs website http://www.avianknowledge.net/tdwg. I think we still need to define occurrence, and I think that Arthur Chapman's "species occurrence data" gets us most of the way there. My sense is that the elaborations need to be expanded a bit more. For example, data collection event. I suggest that we include in the definition some information about time, minimum required data, and so forth. These definitions can be longer and more detailed than the observation definition. So taking data collection event: An event, during or after which at least the minimum required data were recorded. Can we identify the minimum required data? For us it is: who the collector is where the information was collected (and should refer to occurrence information and all of the discussion with it) when the data and time what was observed (and how many) effort distance covered, time spent etc. I'm sure there are other data for the minimum required data and this is worth discussion. We should also discuss the event. For example, one of ours and Bird Studies Canada projects (Project FeederWatch) the event can last 2 days. We also need to think about whether we want to include protocol. In our definitions no protocol (incidental observation) is also a protocol. Anyway, thanks for the improvements on the definition of observation. I (like Lynn) look forward to discussing some of these other issues. Steve At 05:03 PM 2/8/2006 -0500, you wrote: >With only comments from Bob & Arthur (thanks!), the latest version of >observation definitions is as follows: > >"An observation characterizes the evidence for the presence or absence >of an organism or set of organisms through a data collection event at a >location. Observations are not necessarily independent and could be >linked via characteristics such as time, place, protocol, and >co-occurring organisms." > >With the following draft elaborations for various terms (many thanks to >Bob Peet for providing most of these draft definitions): > >1) occurrence > >"Occurrence" has been changed to "evidence for the presence or absence". > >The key idea is that the organism or set of organisms was either >detected or not. We also need to provide an opportunity for the >recorder to note the certainty. > >As an aside, recall we need to support minimalist protocols (e.g. >"organism/community (not)seen in field", "organism heard in field", >"scat seen in field", "tracks seen in field", "museum collection".) > >2) data collection event > >An event, during or after which at least the minimum required data were >recorded. > >3) location > >Ideally, at least geocoordinates plus an accuracy term. Since there is a >considerable amount of historical / legacy data that does not presently >have a georeference yet has valuable information that should be included >in observation databases and shared, we cannot at this time require data >to be in a GIS format. > >I (Lynn) suggest: >(a) Location information be required, preferably geocoordinates and >mapping precision, but if not available then a text description and the >finest level of geolocation using the Darwin Core attributes. > >(b) Location data include the representation of observations as point, >line, or polygon data (with the necessary spatial metadata). > >4) entity > >Dropped from the definition of observation. > >5) could be linked > >Can have a pointer or pointers to other observations, thereby creating >aggregate observations. Note that commonality of date, time, place, >etc. is not sufficient in that the none of the observation authors >explicitly made the connection > > >Please share your comments / thoughts on all of the above definitions >with this email list. > >If people are generally comfortable with the above as working >defintions, then I'd like to propose that we move into the fun part of >identifying attributes to be developed into a schema. > >Thank you - >Lynn > > >Lynn Kutner >Data Management Coordinator >NatureServe >phone: (303) 541-0360 >email: lynn_kutner(a)natureserve.org >http://www.natureserve.org/ > > > > > >_______________________________________________ >Tdwg-obs mailing list >Tdwg-obs(a)lists.tdwg.org >http://lists.tdwg.org/mailman/listinfo/tdwg-obs_lists.tdwg.org _______________________________________________ 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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[Tdwg-obs] TDWG Technical Architecture Group Meeting Call
by Roger Hyam 10 Feb '06

10 Feb '06

Dear Observations List Member, As you may be aware the GUID-1 meeting has now taken place. The outcome of this meeting has wide ranging repercussions for all TDWG standards and their future interoperability. I am therefore calling a Technical Architecture Group meeting as soon as possible to discuss the best way to proceed. This meeting will be able to discuss issues, such as shared vocabularies, which are outside the scope of the GUID project. You can read more about the proposed meeting here: http://www.tdwg.hyam.net/twiki/bin/view/TAG/TagMeeting1 I would be grateful if you would consider whether you might attend or nominate some one to attend. If you would like to discuss the meeting further please join the TAG list to save generating traffic on this list (http://www.tdwg.org/mailinglists.htm) Best wishes, Roger (apologies if you have received this multiple times as it is going to several TDWG lists). -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org roger(a)tdwg.org +44 1578 722782 -------------------------------------

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[Tdwg-lit] MODS
by Anna Weitzman 10 Feb '06

10 Feb '06

Dear All, To help us consider additions we might need to make to the current proposals, attached is an analysis of MODS as it might relate to Level 3; many of the comments may also be relevant for analysis for Level 2. Best wishes, Anna and Chris

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Re: [Tdwg-lit] Level 1
by Anna Weitzman 09 Feb '06

09 Feb '06

Thanks James, Good questions all. As with all standards, the language question is an important one, and not one to be taken lightly. My current opinion (an only my personal one) is that we should decide on the standard elements in one language (and English appears to be the one that continues to surface, whether we all like that or not) and then figure out (and as technology character sets--Unicode not yet being universally available) how to make those work in all languages. I also personally believe that is important to include the source language and characters and to translate (or transliterate) those into other language(s)...whether we choose a single language or go for the UN languages. However, the latter is a long range goal and we rely on those of you who are fluent in those languages to assist us, now, and in making the standards work in other languages (and probably metadata traditions). ISO dates are an interesting question. For taXMLit, we decided that we should capture dates as they are in the original publication and that any conversion/interpretation belongs in another (and later, still to be developed--see the explanation document) layer. For other standards, we might consider a different solution, but for a full content standard, I believe it best to record what is there and then to add one or more interpretations to other standard(s) or opinions for someplace else (which is closely linked and equally easily acceptable). Cheers, Anna >>> Nozomi Ytow <nozomi(a)biol.tsukuba.ac.jp> 09-Feb-2006 2:11:16 PM >>> Dear all, thanks for documents, Anna. The following questions came to my mind. These are relevant to Level 1, but some also relevant to contents of higher levels. Do we assume ASCII only for human-readable portion, or do we allow non-ASCII including east European, Cyrillic and Asian characters? If we allow non-ASCII, do we expect character normalisation (senu Unicode)? Two or more code points for a single character is not uncommon in Unicode. If we allow non-ASCII, do we need to restrict some fields to ASCII, even if the fields values are non-ASCII in the original literature? Do we use standards such as ISO to display date? Cheers, James _______________________________________________ TDWG-Lit mailing list TDWG-Lit(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-lit_lists.tdwg.org

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Re: [Tdwg-obs] Tdwg-obs Digest, Vol 5, Issue 2
by Robert K. Peet 09 Feb '06

09 Feb '06

> From: "Lynn Kutner" <Lynn_Kutner(a)natureserve.org> > "An observation characterizes the evidence for the presence or absence > of an organism or set of organisms through a data collection event at a > location. Observations are not necessarily independent and could be > linked via characteristics such as time, place, protocol, and > co-occurring organisms." I am happy with something close to this. > 3) location > > I (Lynn) suggest: > (a) Location information be required, preferably geocoordinates and > mapping precision, but if not available then a text description and the > finest level of geolocation using the Darwin Core attributes. > > (b) Location data include the representation of observations as point, > line, or polygon data (with the necessary spatial metadata). I agree, however, I would like to include a measure of uncertainty. Darwin Core has such an element, CoordinateUncertaintyInMeters, that would work. "The upper limit of the distance (in meters) from the given latitude and longitude describing a circle within which the whole of the described locality must lie. Use NULL where the uncertainty is unknown, cannot be estimated, or is not applicable." > 5) could be linked > > Can have a pointer or pointers to other observations, thereby creating > aggregate observations. Note that commonality of date, time, place, > etc. is not sufficient in that the none of the observation authors > explicitly made the connection Some revision along these lines would be helpful. From: <tdwg(a)achapman.org> > The word 'protocol' what does this mean in this context? > In your Locality definition a). I don't think you mean Mapping > Precision here - it is only one aspect of accuracy/uncertainy. Also - > not all coordinates will be attached to a map (e.g. GPS). I prefer any > of the the terms 'Uncertainty', 'Accuracy' or 'Maximum Error' (or all > three/four with Precision). They are all slightly different in meaning. See my note above about the Darwin Core element CoordinateUncertaintyInMeters. > > My other suggestion revolves around the mention of Darwin Core here - is > it necessary - some may be using ABCD, etc. and should we necessarily > have the definition tied to a protocol We don't need to be tied to a standard, but the closer we come to being consistent with the rest of the community, the more likely our standard is to be widely accepted. In short, I like following the Darwin Core where it works for us, but I see no need to explicitly refer to the Darwin Core. Neither the Darwin Core or ABCD will work for us when it come to taxonomic identification and there we will need to use the TDWG TCS schema. > From: Hannu Saarenmaa <hsaarenmaa(a)gbif.org> > > "set of organisms" doesn't sound very natural to me. What about "group > of organisms"? However, doesn't the second sentence covers this anyway? "Set of", or "group of", or "assemblage of" all work for me. Bob ====================================================================== 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/ ======================================================================

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Re: [Tdwg-obs] On observation definition / moving forward
by Steve Kelling 09 Feb '06

09 Feb '06

Hello, I really like the improvements made on the definition, and I might suggest that I put it up on the TDWG-obs website http://www.avianknowledge.net/tdwg. I think we still need to define occurrence, and I think that Arthur Chapman's "species occurrence data" gets us most of the way there. My sense is that the elaborations need to be expanded a bit more. For example, data collection event. I suggest that we include in the definition some information about time, minimum required data, and so forth. These definitions can be longer and more detailed than the observation definition. So taking data collection event: An event, during or after which at least the minimum required data were recorded. Can we identify the minimum required data? For us it is: who the collector is where the information was collected (and should refer to occurrence information and all of the discussion with it) when the data and time what was observed (and how many) effort distance covered, time spent etc. I'm sure there are other data for the minimum required data and this is worth discussion. We should also discuss the event. For example, one of ours and Bird Studies Canada projects (Project FeederWatch) the event can last 2 days. We also need to think about whether we want to include protocol. In our definitions no protocol (incidental observation) is also a protocol. Anyway, thanks for the improvements on the definition of observation. I (like Lynn) look forward to discussing some of these other issues. Steve At 05:03 PM 2/8/2006 -0500, you wrote: >With only comments from Bob & Arthur (thanks!), the latest version of >observation definitions is as follows: > >"An observation characterizes the evidence for the presence or absence >of an organism or set of organisms through a data collection event at a >location. Observations are not necessarily independent and could be >linked via characteristics such as time, place, protocol, and >co-occurring organisms." > >With the following draft elaborations for various terms (many thanks to >Bob Peet for providing most of these draft definitions): > >1) occurrence > >"Occurrence" has been changed to "evidence for the presence or absence". > >The key idea is that the organism or set of organisms was either >detected or not. We also need to provide an opportunity for the >recorder to note the certainty. > >As an aside, recall we need to support minimalist protocols (e.g. >"organism/community (not)seen in field", "organism heard in field", >"scat seen in field", "tracks seen in field", "museum collection".) > >2) data collection event > >An event, during or after which at least the minimum required data were >recorded. > >3) location > >Ideally, at least geocoordinates plus an accuracy term. Since there is a >considerable amount of historical / legacy data that does not presently >have a georeference yet has valuable information that should be included >in observation databases and shared, we cannot at this time require data >to be in a GIS format. > >I (Lynn) suggest: >(a) Location information be required, preferably geocoordinates and >mapping precision, but if not available then a text description and the >finest level of geolocation using the Darwin Core attributes. > >(b) Location data include the representation of observations as point, >line, or polygon data (with the necessary spatial metadata). > >4) entity > >Dropped from the definition of observation. > >5) could be linked > >Can have a pointer or pointers to other observations, thereby creating >aggregate observations. Note that commonality of date, time, place, >etc. is not sufficient in that the none of the observation authors >explicitly made the connection > > >Please share your comments / thoughts on all of the above definitions >with this email list. > >If people are generally comfortable with the above as working >defintions, then I'd like to propose that we move into the fun part of >identifying attributes to be developed into a schema. > >Thank you - >Lynn > > >Lynn Kutner >Data Management Coordinator >NatureServe >phone: (303) 541-0360 >email: lynn_kutner(a)natureserve.org >http://www.natureserve.org/ > > > > > >_______________________________________________ >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] On observation definition / moving forward
by Denis Lepage 09 Feb '06

09 Feb '06

I am in support of the suggested "group of organism", rather than "set". I don't believe the second sentence means exactly the same thing. From a database point of vue, sometimes, a group of organism will be reported as one observation record, eg "10 Common Redpolls". The meaning of the second sentence is that observations are usually interlinked, eg, the "10 common redpolls and the 5 pine siskins where observed during the same 5 minute sampling period". I'm also quite happy with the other definitions proposed so far. Denis Denis Lepage, Senior Scientist/Chercheur sénior National Data Center/Centre national des données Bird Studies Canada/Études d'Oiseaux Canada PO Box/B.P. 160, Port Rowan, ON N0E 1M0 519-586-3531 ext. 225, fax/téléc. 519-586-3532 > -----Original Message----- > From: Tdwg-obs-bounces(a)lists.tdwg.org > [mailto:Tdwg-obs-bounces@lists.tdwg.org]On Behalf Of Hannu Saarenmaa > Sent: 09 February 2006 5:14 AM > Cc: Tdwg-obs(a)lists.tdwg.org > Subject: Re: [Tdwg-obs] On observation definition / moving forward > > > "set of organisms" doesn't sound very natural to me. What > about "group of organisms"? However, doesn't the second > sentence covers this anyway? > > Hannu > > > Lynn Kutner wrote: > > >With only comments from Bob & Arthur (thanks!), the latest version of > >observation definitions is as follows: > > > >"An observation characterizes the evidence for the presence > or absence > >of an organism or set of organisms through a data collection > event at a > >location. Observations are not necessarily independent and could be > >linked via characteristics such as time, place, protocol, and > >co-occurring organisms." > > > > > > _______________________________________________ > 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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[Tdwg-lit] Current available schemas
by Anna Weitzman 09 Feb '06

09 Feb '06

Dear All, To enable us to make some comparisons between what is being done currently, we attach a table providing URLs to schemas that are being applied to relevant literature. Feel free to suggest others that we should look at and compare. Best wishes, Anna and Chris

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[Tdwg-lit] Level 3 starting point
by Anna Weitzman 09 Feb '06

09 Feb '06

Dear All, Once again, see the attached. We suggest that taXMLit is a suitable starting-point for this taxonomic content standard. It is a detailed standard, which should allow for markup of any taxonomic literature. The schema can be found at http://www.sil.si.edu/digitalcollections/bca/status.cfm together with an explanatory document and sample files. We will be updating the version of taXMLit and the sample files next week. Similar to the last two messages, please start to comment on this for content, purpose, etc. Thanks Anna & Chris

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