August 2010 - tdwg-tag - lists.tdwg.org

Re: [tdwg-tag] RDF N3
by Kevin Richards 17 Nov '10

17 Nov '10

I like the sound of the 'compactness' of the format, but I worry that there is a lack of tools that support the format (ie browsers, mainly). It is quite nice to naturally navigate the rdf world with a standard browser. But for transfer standards, I suppose this wouldn't matter. Kevin Sent from my HTC ----- Reply message ----- From: "Bob Morris" <morris.bob(a)gmail.com> Date: Sun, Jan 24, 2010 12:08 PM Subject: [tdwg-tag] RDF N3 To: "Technical Architecture Group mailing list" <Tdwg-tag(a)lists.tdwg.org> Let's make N3 be the recommended RDF representation. It is way more compact and human readable than RDF/XML. We could even specify a normative conversion tool if necessary. -- Robert A. Morris Professor of Computer Science (nominally retired) UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 Associate, Harvard University Herbaria email: ram(a)cs.umb.edu web: http://bdei.cs.umb.edu/ web: http://etaxonomy.org/FilteredPush http://www.cs.umb.edu/~ram phone (+1)617 287 6466 _______________________________________________ tdwg-tag mailing list tdwg-tag(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tag ________________________________ Please consider the environment before printing this email Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails. The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz

4 4

Do terms in the http://rs.tdwg.org/dwc/terms/ namespace actually resolve?
by Steve Baskauf 31 Aug '10

31 Aug '10

I was doing some GUID testing using a Linked Data client and I noticed that some Darwin Core terms did not seem to resolve to anything. I ran a test using http://demo.openlinksw.com/rdfbrowser2/ http://api.talis.com/stores/iand-dev1/items/dipper.html http://www5.wiwiss.fu-berlin.de/marbles/ and http://dataviewer.zitgist.com/ I first I looked up http://purl.org/dc/terms/creator and all four clients reported the properties of the term. Then I tried http://rs.tdwg.org/dwc/terms/basisOfRecord and nothing happened with any of them. I ran a Vapour http://validator.linkeddata.org/vapour validation on the basisOfRecord URI and got the following message: Vapour was unable to complete the request due to the following exception: ForbiddenAddress: forbidden request from 98.87.45.8 to http://rs.tdwg.org/dwc/terms/basisOfRecord (resolves to IP 192.38.28.106), internal IP addresses are forbidden I have no idea what that means, but all of this seems to mean that Darwin Core is currently "broken" from a Linked Data point of view. Steve -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: VU Station B 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 343-6707 http://bioimages.vanderbilt.edu

2 1

Unresloved technical issues - proposed decisions.
by joel sachs 31 Aug '10

31 Aug '10

Hi Everyone - Javier and I chatted yesterday about unresolved technical issues. Our primary goal was simplicity. Here are the outcomes. Feel free to suggest something different, if either i) you're planning on developing around your suggestion; or ii) you believe that to not follow your suggestion would be a grave mistake. NOTE: by "app" we mean anything that is writing to the table - could be a smartphone app, could be a web form, could be a screenscraper or tweet-parser. 1. All apps will write to the same table. Each app will need a Google account, which will be given write-access to the table. 2. The occurrence_id will be the row_id assigned by Fusion Tables. This is not seen in the web interface, but is available from the API. 3. To support crowdsourcing of image identification, alternative identifications, arguments, etc., there will be a 2nd table with columns {occurrence_id, scientificName, vernacularName, Kingdom, identifiedBy, identificationResources, identificationRemarks}. One of each of these columns will also exist in the Occurrences table. When the observation is first reported, any identification will be entered in the Occurrences table, with subsequent identifications in the Identifications table. (The main motivation for keeping the initial identification in the Occurrences table is to ease the process for app developers.) 4. Multiple multimedia URLs will be listed in a single column, comma separated. 5. The lat and long columns will be WGS84. If app developers wish, they are welcome to build support for additional datums into their apps, since the apps will have authority to create additional columns. If this doesn't happen, anyone planning to use another datum will need to announce themselves ahead of time, and we will create appropriate columns for them. 6. The table will contain Kingdom, Phylum, Class, Order, and Family columns. Javier will write software to resolve identifications to the Catalog of Life, and to populate the taxonomy columns. If someones want to resolve observations to a different classification, they are free to do so, and are encouraged to publish the results in Fusion Tables. 7. In addition to the identification table, there is scope for creating an Annotations table and front-end, should anyone wish to tackle this. Here's a timetable that would be nice to adhere to: Sept. 1: Final versions of the Occurrences and Identifications tables published to Fusion Tables. Write access will only be granted to developers. These will be the test tables. The day before the bioblitz, they will become the development tables, and test records will be expunged. Sept. 3: Table documentation and sample code for writing to the tables. Sept. 8: Taxanomic resolution, validation, assignment of taxon GUIDS/LSIDs. Sept. 15: At least one Image identification framework in place. Sept. 15 - Sept. 28: Testing and work on visualization and other data-oriented services (e.g. publication as DwC or Linked Data, etc.) Best to all - Joel.

5 11

updated tables
by joel sachs 27 Aug '10

27 Aug '10

I updated the "Occurrences" table by deleting the "occurrence_id" column, since we will be using (the hidden) "row_id" to identify occurrences. I created the "Identifications" table along the lines I described yesterday, with the addition of a "table_id" column. So the key for the table (and guid for occurences) is (table_id, row_id), and we can support data from multiple occurrence tables. a "taxonConceptID" column taxonomy columns The tables are http://tables.googlelabs.com/DataSource?dsrcid=225363 http://tables.googlelabs.com/DataSource?dsrcid=241441 Don't be afraid to try them out - Joel.

1 0

Re: [tdwg-tag] time and space namespaces in Darwin Core
by Bryan 25 Aug '10

25 Aug '10

There is a Droid AP called GPS status the reports dop dilution of precision. I have not looked into how that relates to meters. sent from my Droid On Aug 25, 2010 7:28 PM, "Peter DeVries" <pete.devries(a)gmail.com> wrote: I looked through my iPhone programming book and the iPhone does output an accuracy measure that can be in meters. I don't now if all the applications expose this functionality but I did find one for iPhone / iPad that does. http://gps.motionx.com/iphone/overview/ <http://gps.motionx.com/iphone/overview/>- Pete On Tue, Aug 24, 2010 at 3:44 PM, John Wieczorek <tuco(a)berkeley.edu> wrote: > > Catching up on this... TaxonConcept Knowledge Base <http://www.taxonconcept.org/> / GeoSpecies Knowledge Base <http://lod.geospecies.org/> About the GeoSpecies Knowledge Base ------------------------------------------------------------

1 0

time and space namespaces in Darwin Core
by joel sachs 25 Aug '10

25 Aug '10

All, When representing observation records in RDF, there are advantages to using Dublin Core and Geo (http://www.w3.org/2003/01/geo/wgs84_pos#) namespaces where possible. For example, if we use DC:date, and geo:lat, geo:long, instead of DwC:eventDate, DwC:lat, and DwC:long, then Linked Data browsers can automatically map the records, plot them on a timeline, etc. My question is: What are the disadvantages to doing this? (For example, is this going to break someone's DwC validator?) Thanks - Joel.

4 8

Re: [tdwg-tag] time and space namespaces in Darwin Core
by John Wieczorek 24 Aug '10

24 Aug '10

The partially good news is that if enough information (dwc:geodeticDatum) is given in a Darwin Core-based record, geo:lat/lon can be determined from it. More disturbing to me is that anyone would think geo:lat/lon alone is sufficient for any application, as it carries no notion of uncertainty and therefore fitness for use. Add dwc:coordinateUncertaintyInMeters (or even dwc:coordinatePrecision if you must) to the mix and I would be much happier. On Sun, Aug 8, 2010 at 11:26 PM, <Garry.Jolley-Rogers(a)csiro.au> wrote: > Hi Jim, > Thanks. Had this aside to read in detail later. I think John is > right... As same value with different constraints mean different > interpretations are possible and seems to be the key thing. How are the > values to be interpreted. > > G > > -----Original Message----- > From: Jim Croft [mailto:jim.croft@gmail.com] > Sent: Monday, 9 August 2010 4:12 PM > To: Alexander, Paul (PI, Black Mountain); Harvey, Paul.W (PI, Black > Mountain); Jolley-Rogers, Garry (PI, Black Mountain); Cawsey, Margaret (CES, > Crace); Greg Whitbread > Cc: tuco(a)berkeley.edu > Subject: Fwd: [tdwg-tag] time and space namespaces in Darwin Core > > Did you catch this thread on tdwg-tag? It is an almost exact mirror > of the conversations we have be having in the taxon profile space, but > involving the specimen locational data. > > From John's comments it would appear he is not prepared to accept the > geo: and dwc: lat/long as 'exact match' because, although they are the > same values, they have different constraints (or more precisely one > one has a constraint and one doesn't). > > I wouldn't have picked it but this looks like a case for 'closematch'. > > jim > > > ---------- Forwarded message ---------- > From: John Wieczorek <tuco(a)berkeley.edu> > Date: Mon, Aug 9, 2010 at 3:56 AM > Subject: Re: [tdwg-tag] time and space namespaces in Darwin Core > To: joel sachs <jsachs(a)csee.umbc.edu> > Cc: tdwg-bioblitz(a)googlegroups.com, tdwg-tag(a)lists.tdwg.org > > > There is actually no equivalency between dwc:decimalLatitude and > geo:lat because geo:lat is specified to represent the latitude in the > WGS84 spatial reference system and dwc:decimalLatitude has no such > such restriction. > > On Fri, Aug 6, 2010 at 10:08 AM, joel sachs <jsachs(a)csee.umbc.edu> wrote: > > > > On Fri, 6 Aug 2010, Hilmar Lapp wrote: > > > > > Shouldn't the RDF for DwC link DwC:lat to geo:lat (using some subtype > > > or better yet equivalency relation)? And shouldn't hence Linked Data > > > browsers be able to use DwC:lat in the same way as geo:lat? > > > > > > > Yes. But no Linked Data browser I'm aware of applies > > owl:equivalentProperty assetions before rendering the data. (In fact, > most > > do no reasoning at all.) I agree that, whatever our default display, > > it should include the appropriate mapping statements, either via an > > rdfs:seeAlso or similar link, or directly in the document. > > > > > > Joel. > > > > > > > -hilmar > > > > > > On Aug 6, 2010, at 11:01 AM, joel sachs wrote: > > > > > >> All, > > >> > > >> When representing observation records in RDF, there are advantages > > >> to using Dublin Core and Geo (http://www.w3.org/2003/01/geo/ > > >> wgs84_pos#) > > >> namespaces where possible. For example, if we use DC:date, and > > >> geo:lat, geo:long, instead of DwC:eventDate, DwC:lat, and DwC:long, > > >> then Linked Data browsers can automatically map the records, plot > > >> them on a timeline, etc. > > >> > > >> My question is: What are the disadvantages to doing this? (For > > >> example, is this going to break someone's DwC validator?) > > >> > > >> Thanks - > > >> Joel. > > >> > > > > > > -- > > > =========================================================== > > > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > > > =========================================================== > > > > > _________________ > Jim Croft ~ jim.croft(a)gmail.com ~ +61-2-62509499 ~ > http://www.google.com/profiles/jim.croft > 'A civilized society is one which tolerates eccentricity to the point > of doubtful sanity.' > - Robert Frost, poet (1874-1963) > > Please send URIs, not attachments: > http://www.gnu.org/philosophy/no-word-attachments.html >

5 11

Re: [tdwg-tag] time and space namespaces in Darwin Core
by Bryan 24 Aug '10

24 Aug '10

If there is likely to be multiple coordinate systems can we have a column that defaults to wgs84 but may be reset to other systems? Does someone have a table that could be given to data collectors for estimating uncertainty? The variables in this case are limited. sent from my Droid On Aug 12, 2010 2:04 AM, "Javier de la Torre" <jatorre(a)gmail.com> wrote: +1 for bioblitz. I will add that because Fusion tables use WGS84 for geometries it is important that we don't mix them. We will be relying on the spatial capabilities on fusion tables for data visualization. Javier www.vizzuality.com On 12/08/2010, at 03:52, joel sachs <jsachs(a)csee.umbc.edu> wrote: > On Mon, 9 Aug 2010, Javier de ...

2 1

Proposed Darwin Core term additions and changes: individualRemarks and establishmentMeans
by Steve Baskauf 11 Aug '10

11 Aug '10

In http://code.google.com/p/darwincore/issues/detail?id=70 I proposed addition of the class Individual to Darwin Core. In the discussion of that proposal, the question was raised as to which existing DwC terms should be a part of this class if it were added. After considerable thought and some work in developing RDF representations for Individuals, I believe that the term establishmentMeans should be a member of the proposed class. It has also become clear to me that if the class is introduced, there is a need for the term individualRemarks which would serve a parallel purpose to other xxRemarks terms in DwC. I have provided implementation examples in the recommendations, which can be found at http://code.google.com/p/darwincore/issues/detail?id=80 and http://code.google.com/p/darwincore/issues/detail?id=81 If you would like to discuss these proposals, please post on the tdwg-contents list or add comments to the Google Code wiki. I have cross-posted to the tdwg-tag list, but I think any discussion would be better held on the tdwg-content list, so please post there. Steve Baskauf -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: VU Station B 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 343-6707 http://bioimages.vanderbilt.edu

1 1

provenance chains and DwC:recordedBy
by joel sachs 06 Aug '10

06 Aug '10

All, In preparation for the tdwg bioblitz, I'd like to configure our Spotter tool (http://spire.umbc.edu/spotter) to compose DwC records. Currently, it uses an observation ontology that we whipped up a few years ago. (Here's an illustrative record - http://spire.umbc.edu/spotter/observation/data.php?record=1534) For the most part, the mapping is straightforward. However, I'm wondering about two terms: "hasObserver" and "hasReporter". We distinguished between these two terms to accommodate situations where a student makes an observation, but her teacher reports it. Similarly, in a bioblitz event, one model is that a survey team leader will fill out and submit a spreadsheet comprised of the observations made by members of the survey team. Both these terms seem to map to DwC:recordedBy. According to http://rs.tdwg.org/dwc/terms/#recordedBy, "The primary collector or observer, especially one who applies a personal identifier (recordNumber), should be listed first." So if we simply listed observer followed by reporter, we would comply with the spec. Of course, the ordering would be lost in typical rdf representations, since triples are considered unordered. And whether in rdf or in text, the distinction between observer and reporter would be pretty much lost. Since one of the goals of the bioblitz is figuring out good ways to use DwC in citizen science, I'm interested in opinions on whether we should preserve the observer/reporter distinction, and include these non-DwC terms in the bioblitz data profile. Many thanks - Joel.

4 5