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data provenance; was Re: Updated TDWG BioBlitz RDF Example with Pivot View and Data Browsing
by Bob Morris 01 Mar '11

01 Mar '11

Your arguably reasonable recoding of the geo uri's of your example illustrates an issue on which so much metadata is silent: provenance. Once exposed, it is probably impossible for someone to know how the uncertainty (or any other data that might be the subject of opinion or estimate) was determined and whether the data is fit for some particular purpose, e.g. that the species were observed near each other. BTW, the IETF geo proposal was adopted in 2010, in the final form given at http://tools.ietf.org/html/rfc5870 . One interesting point is http://tools.ietf.org/html/rfc5870#section-3.4.3 which says "Note: The number of digits of the values in <coordinates> MUST NOT beinterpreted as an indication to the level of uncertainty." The section following is also interesting, albeit irrelevant for your procedure. It implies that when uncertainty is omitted (and therefore unknown), then "geo:41.53000000,-70.67000000" and "geo:41.53,-70.67" identify the same geo resource. Bob Morris On Wed, Feb 23, 2011 at 4:56 PM, Peter DeVries <pete.devries(a)gmail.com>wrote: > > [...] > > 5) I added in my proposed "area" so that it is easy to see what species > were observed near each other. Since there was no measure of radius in these > longitude and latitudes I made the radius 100 meters. > Normally I would estimate the radius for a GPS reading to be within 10 > meters but some of these observations were made where the GPS reading was > taken and the readings were given only to two decimals. > > Area = long, lat; radius in meters following the ietf proposal but with the > precision of the long and lat standardized > example "geo:41.53000000,-70.67000000;u=100" > > [...] > -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 Associate, Harvard University Herbaria email: morris.bob(a)gmail.com web: http://efg.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram phone (+1) 857 222 7992 (mobile)

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More Strange Monkey Business-like things in GBIF KOS Document
by Peter DeVries 01 Mar '11

01 Mar '11

More Strange Monkey Business-like things in GBIF KOS Document. Does this accurately characterize my project? "in the GeoSpecies project104 based on a small purpose-built ontology105 of mosquito-borne human pathogens." Did they bother to read any of the seven other examples on this page? Or here http://www.taxonconcept.org/ or here http://www.delicious.com/kidehen/pivot_collection_app+linked_geo_species or here http://www.slideshare.net/pjdwi/biodiversity-informatics-on-the-semantic-web Also note that this particular link they used in the document 104 does not work http://about.geospecies.org/index.htm While this http://about.geospecies.org/ or this does http://about.geospecies.org/index.html Also the "small" TaxonConcept SPARQL endpoint has ~27 million triples. It might also be useful to explain how reasoning can be used on the larger data sets. Do they have an example of reasoning that works on a data set over 100 million triples? Is there some reason why there is so much "push" towards specialized near proprietary solutions like LSID's and LOD unfriendly vocabularies? Respectfully, - Pete -- --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 TaxonConcept Knowledge Base <http://www.taxonconcept.org/> / GeoSpecies Knowledge Base <http://lod.geospecies.org/> About the GeoSpecies Knowledge Base <http://about.geospecies.org/> ------------------------------------------------------------

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Updated TDWG BioBlitz RDF Example with Pivot View and Data Browsing
by Peter DeVries 23 Feb '11

23 Feb '11

I have updated my earlier revision of the TDWG BioBlitz RDF. I commend Joel for his RDF and think that any suboptimality was because of problems in trying to use the existing Darwin Core as Linked Data. Some earlier issues that have been fixed in the new examples are: 1) The names for people were not standardized. Even as a text string you could not find who collected what. To fix this I created URI's for all the individuals involved and linked the occurrences to the URI for the person that made the observation 2) The names for species were not standardized or spell checked. It took a while but I was able to figure out what I think people "meant" by the various name and linked them to species concepts. For those occurrences with multiple identifications, I linked the last identification to the occurrences species concept. *Future BioBlitz's might benefit from a pick list at least to genus. 3) Virtuoso out of the box does not recognize "associatedMedia" as an image that can be displayed. In order to get these to show up on the map view I had to add each image as a foaf:depiction. Also associatedMedia is a bit vague and this should probably be broken into different media types like images, sounds etc. 4) In my other RDF representations I make statement about the geonames locations in which the species concept was observed so the continent, state and county have "expectationsOf" the species and the species is "expectedIn" those areas. I have added these statements to the example RDF so that both the locations and the species concepts are linked to the occurrences. 5) I added in my proposed "area" so that it is easy to see what species were observed near each other. Since there was no measure of radius in these longitude and latitudes I made the radius 100 meters. Normally I would estimate the radius for a GPS reading to be within 10 meters but some of these observations were made where the GPS reading was taken and the readings were given only to two decimals. Area = long, lat; radius in meters following the ietf proposal but with the precision of the long and lat standardized example "geo:41.53000000,-70.67000000;u=100" The example data are available at the following URL's Occurrences: http://lod.taxonconcept.org/tdwg2010bioblitz/TechnoBioblitzOccurrences_date… People: http://lod.taxonconcept.org/people/tdwg2010bioblitz.rdf This bit.ly link will show clickable map with all the occurrences. (It is a little slow to load) The actual URL is < http://lsd.taxonconcept.org/isparql/view/?query=DESCRIBE%20%3Fx%20WHERE%20%… > But I don't expect that will go through everyone's emails correctly. This Pivot view shows occurrences by investigator http://bit.ly/eW3fgm Here is are view of two of the records, note how you can browse between people, species concepts, identifications, areas etc. http://lsd.taxonconcept.org/describe/?url=http://www.cs.umbc.edu/~jsachs/oc…<http://lsd.taxonconcept.org/describe/?url=http://www.cs.umbc.edu/~jsachs/oc…> http://lsd.taxonconcept.org/describe/?url=http://www.cs.umbc.edu/~jsachs/oc… Here is a browsable view of one of the areas bit.ly http://bit.ly/hBtVFL http://lsd.taxonconcept.org/describe/?url=geo:41.53000000,-70.67000000;u%3D… Here is the view of the species concept for the Honey Bee that is now linked to these occurrence records. http://bit.ly/g1zzJC In summary, I think it make sense to follow LOD best practices because this maximizes the utility of the data and allows you to take advantage of all the available tools. <http://bit.ly/eW3fgm>Respectfully, - Pete --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 TaxonConcept Knowledge Base <http://www.taxonconcept.org/> / GeoSpecies Knowledge Base <http://lod.geospecies.org/> About the GeoSpecies Knowledge Base <http://about.geospecies.org/> ------------------------------------------------------------

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Example RDF for Occurrence Records following Linked Open Data practices
by Peter DeVries 21 Feb '11

21 Feb '11

I thought I would explain how I have been marking up occurrence records in RDF in this blog post. http://www.taxonconcept.org/taxonconcept-blog/2011/2/21/species-occurrence-… The quad store view of the different RDF entities mentioned in the blog can be seen here: Via this bit.ly bundle http://bit.ly/fnlTZd * Note that some of these links get change in email so you might want to use the bit.ly bundle above The RDF page: http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f… The Occurrence: http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f… The Area: http://lsd.taxonconcept.org/describe/?url=geo:44.86528100,-87.23147800;u=10 The Species Concept: http://lsd.taxonconcept.org/describe/?url=http://lod.taxonconcept.org/ses/I… The Individual: http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f… The Identification: http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f… The Continent: http://lsd.taxonconcept.org/describe/?url=http://sws.geonames.org/6255149/ The County: http://lsd.taxonconcept.org/describe/?url=http://sws.geonames.org/5250768/ Although the exact format of these could be changed there are several existing advantages and some possible future advantages. 1) Each data provider could expose their own data to the web without a central authority. This could be in the form of RDF, RDFa, or as gzipped RDF dump files. (records.rdf.gz) They would be automatically discoverable on the LOD cloud. A third party service could add value by pointing to the various repositories, perhaps with an annotation system like or as part of CKAN. ( http://ckan.net/) 2) Data validation in terms of being "well-formed" could be checked with the existing RDF and RDFa validators. http://www.w3.org/RDF/Validator/ http://validator.w3.org/ 3) The next level of validation e.g: Is this a valid geographic coordinate? Does the coordinate match the geographical names listed *(You could even have a service that takes the geo area and determines the correct geographic names etc.) Does the scientific name match a known species? Are the other required fields present and well formed. Is this a new record for that species in that specific geographic area Would have to be done by a validator created for the community, but it would benefit from the existing tools. 4) All the third party LOD tools and services would be able to use these records. Respectfully, - Pete -- --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 TaxonConcept Knowledge Base <http://www.taxonconcept.org/> / GeoSpecies Knowledge Base <http://lod.geospecies.org/> About the GeoSpecies Knowledge Base <http://about.geospecies.org/> ------------------------------------------------------------

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ShootOut at the Not OK Corral: namespaces in OWL (technical)
by Bob Morris 04 Feb '11

04 Feb '11

If you have ever been in pain over namespaces in OWL ontologies and RDF data, you may want to read this year-old day-time television soap opera script, errr...ummmm... I mean, highly technical discussion about namespaces. My guess is that this pain will be with us for a long time. http://comments.gmane.org/gmane.org.w3c.semantic-web/11878 FWIW, gmane seems to be a rather nice syndication mechanism for mailing lists, making it quite a bit easier than looking in gnu-mailman archives to follow old threads . My only complaint is that you have to poke a bit to find the originals (whereupon you are grateful to gmane) Bob -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 Associate, Harvard University Herbaria email: morris.bob(a)gmail.com web: http://efg.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram phone (+1) 857 222 7992 (mobile)

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Audubon Core NameSpace
by Bob Morris 03 Feb '11

03 Feb '11

We dropped discussion of this, and I know Steve Baskauf and perhaps others want to start using it with minimal risk of having to redo data. I found little consensus in the discussion, and no compelling reason why the prefix had to end in "c". Therefore, I'd like to put back(?) on the table and resolve it quickly. Gail or others will guide us as to whether the Executive Committee cares about what we settle on: http://adbn.tdwg.org recommended prefix adbn --Bob -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 Associate, Harvard University Herbaria email: morris.bob(a)gmail.com web: http://efg.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram phone (+1) 857 222 7992 (mobile)

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Bioblitz as rdf: does this make sense?
by joel sachs 18 Jan '11

18 Jan '11

Hi Everyone, I've posted rdf of the bioblitz data. It's at http://www.cs.umbc.edu/~jsachs/occurrences/TechnoBioblitzOccurrences.rdf . Individual occurrences can be retrieved via http://www.cs.umbc.edu/~jsachs/occurrences/[occurrence_id] e.g. http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1835 Individual identifications can be retrieved via http://www.cs.umbc.edu/~jsachs/identifications/[identification_id] e.g. http://www.cs.umbc.edu/~jsachs/identifications/tdwg2010bioblitz_1835_id_1 The scripts behind this are on the kludgy side, so reports of errors and abnormalities will be warmly welcomed. Implicit in each of the following notes is the question "Is this a good way to do it?": 1. The data is "normalized" w.r.t. identification. "Normalized" is in quotes because I mean it in the sense that Steve Baskauf was using in his Fall 2010 series of posts. His meaning of the term makes sense to me, but many people (e.g. the OBO folks), take "normalized ontology" to mean "disentangled" (i.e. no multiple inheritance.) As an example, here's an occurrence with two crowdsourced determinations: http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1644 2. I used sequential integers for observation and identification IDs; in practice, a mechanism needs to be in place to prevent two people from assigning the same id to their respective identifications. 3. My answer to Cam Webb's Question #1 from http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001720.html is "both". In other words, just as "Joel Sachs" is both me and also my name, so http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1668 is both an occurrence and an occurrence_id, expressed as: --- <dwc:Occurrence rdf:about="http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1644"> <dwc:occurrenceID> http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1644 </dwc:occurrenceID> <blah blah blah/> </dwc:Occurrence> --- 4. I was surprised to see that the Darwin Core Identification class has no "occurrenceID" or "specimenID" term. How is one supposed to tie an identification to an observation (assuming the identification is not in-lined, of course)? DeVries and Baskauf each mint their own terms for doing this (txn:identificationHasOccurrence, and sernec:basedOnOccurrence, respectively); I used dwc:occurrenceID as if it were a record level term. 5. We had scope for multiple taxonConceptID columns in the Fusion table, and assigned lsids where possible. I also mean to work with Pete to assign GUIDs from taxoncocept.org. In addition, I assigned ethan taxon concept ids, which look like this: http:.//spire.umbc.edu/ethan/Coffea_arabica In their argument over opaque vs. transparent taxonCoceptIDs, I was sympathetic to both Pete's and Gregor's arguments. Ultimately, if the tooling exists to always display the rdfs:labels every time I'm loooking at a list of opaqueIDs, then transparent IDs are unnecessary. But, for now, it's really helpful to look at an ID and know what it's referring to. (For species names not in the spire database, the rdf returned by http:.//spire.umbc.edu/ethan/$name is simply an rdfs:seeAlso to http://http://gni.globalnames.org/name_strings?search_term=$name) 6. It was easy to assert membership in RDF classes corresponding to various Cape Cod categories of concern - invasive species, threatenened species, indicators, etc. You can see these classes at http://spire.umbc.edu/ontologies/lists (Information of where these lists come from is included as rdfs:comments. I'll add further documentation, e.g. links to eml files.) Note that "ThingOfConcern" is defined as the superclass of all the other classes in the collection. The idea here is that people can create their own "ThingOfConcern" class, and then query for observations that are of concern to them. You can see sample sparql queries at http://www.csee.umbc.edu/~jsachs/occurrences/queries/sample.txt As an aside, I think we, as a community, should come up with a biodiversity benchmark suite of rdf data and corresponding sparql queries, that can be used to test the suitability and scalability of semantic web knowledge bases. I'll take this up in a future post (unless someone beats me to it). Comments, questions, and better ideas are welcome. Thanks - Joel.

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Spell checker for scientific names?
by Tony.Rees＠csiro.au 18 Jan '11

18 Jan '11

joel sachs wrote: > BTW, does anyone know a good spell checker for scientific names? Sounds like you may be interested in accessing my TAXAMATCH algorithm which is installed over my IRMNG database of generic and species names, available here: http://www.cmar.csiro.au/datacentre/irmng/ The database is around 90%+ complete for generic names (including non-valid ones) and maybe 50% for valid species names plus some synonyms (the latter based mainly on Catalogue of Life 2006 edition, with more to come). If you enter a single name for checking, fuzzy matches are automatically returned together with any exact matches. If you enter e.g. a line delimited list, the first pass does exact matches only (for speed) with the option to do a fuzzy search on any name not matched as a pre-formatted link. Currently it returns human-readable HTML but I will probably make an option for XML return if there is sufficient demand. Take a look and let me know if this is of interest, or if not, what you would prefer to see... Regards - Tony Rees, Tasmania ________________________________________ From: tdwg-content-bounces(a)lists.tdwg.org [tdwg-content-bounces(a)lists.tdwg.org] On Behalf Of joel sachs [jsachs(a)csee.umbc.edu] Sent: Wednesday, 19 January 2011 6:42 AM To: Peter DeVries Cc: tdwg-content(a)lists.tdwg.org Subject: Re: [tdwg-content] Bioblitz as rdf: does this make sense? Pete - I'm glad you're doing cool things with the data. A few comments/answers/questions ... i. The quests for consistently used canonical URIs, and consistently used canonical names are both, for now, somewhat quixotic, and I'm not sure one is more so than the other. GNA/GNI seems to be pursuing both. Is that a fair assessment? ii. I used opaque taxon concept URIs where they were readily available. Laziness motivated me to also use transparent identifiers for a. making sure each taxonConcept had an rdf:resource as an identifier, and b. asserting membership in the various rdfs:classes that I defined. But laziness has its drawbacks, and you point out a few of them. I think best practice when using either names or transparent URIs as identifiers would be to first run them through a spell checker and normalizer that would produce consistent usage of upper and lowe case characters, and probably drop authorship. Of course, this would produce some false positives when doing any sort of querying. But using UUIDs produces false negatives since they're not in common use. If we (as a community) follow through on the enthusiasm for creating competency cases that we showed in the Fall, it would be interesting to consider each case from the question of what's worse - false positives or false negatives. In any event, false positives can be weeded out by using the full scientific names and contextual information in the record, whereas false negatives may never be discovered. BTW, does anyone know a good spell checker for scientific names? iii. Mapping names to opaque URIs doesn't resolve the problems you raise below. Will the identifer for Carpodacus mexicanus be the same as the identifier for Carpodacus mexicanus (Statius Muller, 1776)? How about Arabis laevigata (Muhl. ex Willd.) Poir. vs. Arabis laevigata ? If yes, then why noy just use normalized names as identifiers? If no, then we'll get false negatives in the sorts of SPARQL queries that I gave at http://www.csee.umbc.edu/~jsachs/occurrences/queries/ BTW, is there a lookup service for taxonconcept.org identifiers (i.e. give a list of names, get a list of identifiers)? iv. In what sense do you see Darwin Core as being deficient as a semantic web representation? Regards - Joel. On Thu, 13 Jan 2011, Peter DeVries wrote: > Thanks Joel, > > Here is one of the BioBlitz Occurrence Records marked up with Darwin Core > > http://lsd.taxonconcept.org/describe/?url=http://www.cs.umbc.edu/~jsachs/oc… > > Here is one of the TaxonConcept Records marked up in the txn vocabulary > http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f… > > Some people have trouble with how the %23 above is escaped in their email, > they might like this bit.ly bundle > better.<http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f…> > <http://lsd.taxonconcept.org/about/html/http/ocs.taxonconcept.org/ocs/f52244…> > http://bit.ly/hZdUpP > > <http://bit.ly/hZdUpP>Also an issue to discuss is that identifications are > to both a name and a concept so > > Should these should be the same dwc:taxonConcepts > > http://spire.umbc.edu/ethan/Apis_mellifera > http://spire.umbc.edu/ethan/Apis_Mellifera > ==> http://bit.ly/g1zzJC (Apis mellifera se:z9oqP) > > http://spire.umbc.edu/ethan/Ascelpius_syruaca > http://spire.umbc.edu/ethan/Asclepias_syriaca > ==> HTML page http://lod.taxonconcept.org/ses/tTEIq.html Concept View > Bit.ly http://bit.ly/dJHJqj > > http://spire.umbc.edu/ethan/Aster_nova-belgii > http://spire.umbc.edu/ethan/Aster_nova-gelgii > > http://spire.umbc.edu/ethan/Baccharis_halimifolia > http://spire.umbc.edu/ethan/Baccharis_halimifolia_L. > > http://spire.umbc.edu/ethan/Bartonia_virginia > http://spire.umbc.edu/ethan/Bartonia_virginica > > http://spire.umbc.edu/ethan/Branta_canadensis > http://spire.umbc.edu/ethan/Branta_canadensis_(Linnaeus,_1758) > > http://spire.umbc.edu/ethan/Carex_pennsylvanica > http://spire.umbc.edu/ethan/Carex_pensylvanica > > http://spire.umbc.edu/ethan/Cyperus_esculantus > http://spire.umbc.edu/ethan/Cyperus_Esculantus > http://spire.umbc.edu/ethan/Cyperus_esculentus > http://spire.umbc.edu/ethan/Cyperus_esculentus_L. > > http://spire.umbc.edu/ethan/Carpodacus_mexicanus > http://spire.umbc.edu/ethan/Carpodacus_mexicanus_(Statius_Muller,_1776) > >> From the taxonconcepts their should be a link to the various name strings. > > vs. modeling the namestring as the concept. > > Also I think that DarwinCore is good for somethings but maybe not as a > semantic web representation. > > Respectfully, > > - Pete > > > On Thu, Jan 13, 2011 at 6:53 AM, joel sachs <jsachs(a)csee.umbc.edu> wrote: > >> Pete, >> Thanks - I corrected the geo properties. >> Joel. >> >> >> >> >> On Wed, 12 Jan 2011, Peter DeVries wrote: >> >> Hi Joel, >>> >>> Cool :-) >>> >>> I just loaded this into my SPARQL endpoint. >>> >>> In the named graph >>> urn:org:linkedopenspeciesdata:dataspace:tdwg2010bioblitz >>> >>> It consists of 19,990 Triples >>> >>> Here is one of the dwc:taxonConceptID entries. >>> >>> *About: http://spire.umbc.edu/ethan/Ampelopsis_brevipedunculata* >>> >>> http://lsd.taxonconcept.org/describe/?url=http://spire.umbc.edu/ethan/Ampel… >>> >>> *About: http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1627* >>> < >>> http://lsd.taxonconcept.org/describe/?url=http://spire.umbc.edu/ethan/Ampel… >>>> >>> >>> http://lsd.taxonconcept.org/describe/?url=http://www.cs.umbc.edu/~jsachs/oc… >>> >>> >>> >>> < >>> http://lsd.taxonconcept.org/describe/?url=http://www.cs.umbc.edu/~jsachs/oc… >>>> This >>> should give you an a count of occurrences. >>> >>> SELECT count(*) WHERE {?s a <http://rs.tdwg.org/dwc/terms/#Occurrence>}; >>> >>> = 1882 >>> >>> SELECT count(*) WHERE {?s a <http://rs.tdwg.org/dwc/terms/#taxonConceptID >>>> }; >>> >>> This should give you a list of occurrences >>> >>> >>> http://lsd.taxonconcept.org/describe/?url=http://rs.tdwg.org/dwc/terms/%23O… >>> >>> If this did not come through your email system try the bit.ly. >>> >>> http://bit.ly/g9BcoL >>> >>> I tried the following that should have given me a google map of all the >>> occurrences but it did not result in the map. >>> >>> DESCRIBE ?x WHERE { >>> ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> < >>> http://rs.tdwg.org/dwc/terms/#Occurrence>. >>> } >>> >>> I looked that the RDF and I think I see the problem. >>> >>> In the RDF >>> >>> <geo:latitude> >>> 41.53 >>> </geo:latitude> >>> >>> <geo:longitude> >>> -70.67 >>> </geo:longitude> >>> >>> Should be >>> >>> <geo:lat> >>> 41.53 >>> </geo:lat> >>> >>> <geo:long> >>> -70.67 >>> </geo:long> >>> >>> See http://www.w3.org/2003/01/geo/ >>> >>> I did the following query to get a list of all the dwc:taxonConceptID's >>> and >>> have attached them as a .txt file. >>> >>> select distinct ?o WHERE {?s < >>> http://rs.tdwg.org/dwc/terms/#taxonConceptID> >>> ?o} >>> >>> Pretty neat :-) >>> >>> There are some things that I will get back to Joel on. >>> >>> Here is where you can manually enter a SPARQL query. Click on "Advanced" >>> for >>> the entry window. >>> >>> http://lsd.taxonconcept.org/isparql/ >>> >>> Respectfully, >>> >>> - Pete >>> >>> >>> >>> On Wed, Jan 12, 2011 at 5:55 PM, joel sachs <jsachs(a)csee.umbc.edu> wrote: >>> >>> Hi Everyone, >>>> >>>> I've posted rdf of the bioblitz data. It's at >>>> http://www.cs.umbc.edu/~jsachs/occurrences/TechnoBioblitzOccurrences.rdf. >>>> >>>> Individual occurrences can be retrieved via >>>> http://www.cs.umbc.edu/~jsachs/occurrences/[occurrence_id]<http://www.cs.umbc.edu/~jsachs/occurrences/%5Boccurrence_id%5D> >>>> e.g. http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1835 >>>> >>>> Individual identifications can be retrieved via >>>> http://www.cs.umbc.edu/~jsachs/identifications/[identification_id]<http://www.cs.umbc.edu/~jsachs/identifications/%5Bidentification_id%5D> >>>> e.g. >>>> http://www.cs.umbc.edu/~jsachs/identifications/tdwg2010bioblitz_1835_id_1 >>>> >>>> The scripts behind this are on the kludgy side, so reports of errors and >>>> abnormalities will be warmly welcomed. >>>> >>>> Implicit in each of the following notes is the question "Is this a good >>>> way to do it?": >>>> >>>> 1. The data is "normalized" w.r.t. identification. "Normalized" is in >>>> quotes because I mean it in the sense that Steve Baskauf was using in his >>>> Fall 2010 series of posts. His meaning of the term makes sense to me, but >>>> many people (e.g. the OBO folks), take "normalized ontology" to mean >>>> "disentangled" (i.e. no multiple inheritance.) >>>> As an example, here's an occurrence with two crowdsourced determinations: >>>> http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1644 >>>> >>>> 2. I used sequential integers for observation and identification IDs; in >>>> practice, a mechanism needs to be in place to prevent two people from >>>> assigning the same id to their respective identifications. >>>> >>>> 3. My answer to Cam Webb's Question #1 from >>>> http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001720.html >>>> is "both". In other words, just as "Joel Sachs" is both me and also my >>>> name, so >>>> http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1668 is both >>>> an occurrence and an occurrence_id, expressed as: >>>> --- >>>> <dwc:Occurrence >>>> rdf:about=" >>>> http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1644"> >>>> <dwc:occurrenceID> >>>> http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1644 >>>> </dwc:occurrenceID> >>>> <blah blah blah/> >>>> </dwc:Occurrence> >>>> --- >>>> >>>> 4. I was surprised to see that the Darwin Core Identification class has >>>> no >>>> "occurrenceID" or "specimenID" term. How is one supposed to tie an >>>> identification to an observation (assuming the identification is not >>>> in-lined, of course)? DeVries and Baskauf each mint their own terms for >>>> doing this (txn:identificationHasOccurrence, and >>>> sernec:basedOnOccurrence, >>>> respectively); I used dwc:occurrenceID as if it were a record level term. >>>> >>>> 5. We had scope for multiple taxonConceptID columns in the Fusion table, >>>> and assigned lsids where possible. I also mean to work with Pete to >>>> assign >>>> GUIDs from taxoncocept.org. In addition, I assigned ethan taxon concept >>>> ids, which look like this: >>>> http:.//spire.umbc.edu/ethan/Coffea_arabica >>>> >>>> In their argument over opaque vs. transparent taxonCoceptIDs, I was >>>> sympathetic to both Pete's and Gregor's arguments. Ultimately, if the >>>> tooling exists to always display the rdfs:labels every time I'm loooking >>>> at a list of opaqueIDs, then transparent IDs are unnecessary. But, for >>>> now, it's really helpful to look at an ID and know what it's referring >>>> to. >>>> >>>> (For species names not in the spire database, the rdf returned by >>>> http:.//spire.umbc.edu/ethan/$name >>>> is simply an rdfs:seeAlso to >>>> http://http://gni.globalnames.org/name_strings?search_term=$name) >>>> >>>> 6. It was easy to assert membership in RDF classes corresponding to >>>> various Cape Cod categories of concern - invasive species, threatenened >>>> species, indicators, etc. You can see these classes at >>>> http://spire.umbc.edu/ontologies/lists (Information of where these lists >>>> come from is included as rdfs:comments. I'll add further documentation, >>>> e.g. links to eml files.) >>>> >>>> Note that "ThingOfConcern" is defined as the superclass of all the other >>>> classes in the collection. The idea here is that people can create their >>>> own "ThingOfConcern" class, and then query for observations that are of >>>> concern to them. You can see sample sparql queries at >>>> http://www.csee.umbc.edu/~jsachs/occurrences/queries/sample.txt >>>> >>>> >>>> As an aside, I think we, as a community, should come up with a >>>> biodiversity benchmark suite of rdf data and corresponding sparql >>>> queries, >>>> that can be >>>> used to test the suitability and scalability of semantic web knowledge >>>> bases. I'll take this up in a future post (unless someone beats me to >>>> it). >>>> >>>> Comments, questions, and better ideas are welcome. >>>> >>>> Thanks - >>>> Joel. >>>> >>>> _______________________________________________ >>>> tdwg-content mailing list >>>> tdwg-content(a)lists.tdwg.org >>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content >>>> >>>> >>> >>> >>> -- >>> --------------------------------------------------------------- >>> Pete DeVries >>> Department of Entomology >>> University of Wisconsin - Madison >>> 445 Russell Laboratories >>> 1630 Linden Drive >>> Madison, WI 53706 >>> TaxonConcept Knowledge Base <http://www.taxonconcept.org/> / GeoSpecies >>> Knowledge Base <http://lod.geospecies.org/> >>> About the GeoSpecies Knowledge Base <http://about.geospecies.org/> >>> ------------------------------------------------------------ >>> >>> > > > -- > --------------------------------------------------------------- > Pete DeVries > Department of Entomology > University of Wisconsin - Madison > 445 Russell Laboratories > 1630 Linden Drive > Madison, WI 53706 > TaxonConcept Knowledge Base <http://www.taxonconcept.org/> / GeoSpecies > Knowledge Base <http://lod.geospecies.org/> > About the GeoSpecies Knowledge Base <http://about.geospecies.org/> > ------------------------------------------------------------ > _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content

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Fwd: Annotation Ontology best practice relation for linking to image/machine-opaque docs? biomedical use case
by Peter DeVries 14 Jan '11

14 Jan '11

This discussion of what specific meanings to assign to various widely used predicates reminds me how often this list seems to prefer operating only within itself. A number of these kinds of issues have been discussed elsewhere. The argument has always been made that we should use standards but when those standards are not those proposed on this list they seem to be ignored. Whether it is the appropriate use of rdfs:seeAlso or other existing widely used vocabularies. Note below a separate Annotations vocabulary. Respectfully, - Pete ---------- Forwarded message ---------- From: Tim Clark <tim_clark(a)harvard.edu> Date: Mon, Jan 10, 2011 at 1:34 PM Subject: Re: best practice relation for linking to image/machine-opaque docs? biomedical use case To: "M. Scott Marshall" <mscottmarshall(a)gmail.com> Cc: HCLS IG <public-semweb-lifesci(a)w3.org>, public-lod(a)w3.org, Daniel Rubin <dlrubin(a)stanford.edu>, "John F. Madden" <john.madden(a)duke.edu>, Vasiliy Faronov <vfaronov(a)gmail.com>, Toby Inkster <tai(a)g5n.co.uk>, Peter DeVries < pete.devries(a)gmail.com>, Tim Berners-Lee <timbl(a)w3.org>, Paolo Ciccarese < paolo.ciccarese(a)gmail.com>, Anita de Waard <A.dewaard(a)elsevier.com>, Maryann Martone <maryann(a)ncmir.ucsd.edu> Hi Scott, For referring to a portion of an image, let me point you to work in my group done in collaboration with HCLS Scientific Discourse Task, UCSD, Elsevier, and one of the major pharmas. Paolo Ciccarese is the main author, and this work is based on the earlier W3C project Annotea. AO, Annotation ontology, here: http://code.google.com/p/annotation-ontology/, presented at Bio Ontologies 2010, and full-length paper in press at BMC Bioinformatics. Bio Ontologies 2010 slides here: http://www.slideshare.net/paolociccarese/ao-annotation-ontology-for-science… AO uses a special subclass of Selector to specify the part of the document (image) being referred to. see here for Selectors: http://code.google.com/p/annotation-ontology/wiki/Selectors and here for an example of image annotation: http://code.google.com/p/annotation-ontology/wiki/AnnotationTypes Best Tim On Jan 10, 2011, at 11:30 AM, M. Scott Marshall wrote: > [Scott dusts off old use case and pulls from the shelf. Adjusts > subject of thread. Was: best practice for referring to PDF] > > In Health Care and Life Science domains, image data is a common form > of data under discussion so a best practice for referring to an image > or to an (extractable) feature *within* an image would cover a > fundamental need in biomedicine to point to 'raw' data as evidence (as > well as giving meaning to the raw data!). > > A clinical example from breast cancer: > There is a scan that produces an image that contains features referred > to by the radiologist as 'microcalcifications', which can be > indicative of the presence of a tumor. > > I can think of a few scenarios that would refer to the image data > (mammogram). There are probably more: > 1) The radiology report (in RDF) asserts the presence of > microcalcifications and refers to the entire image as evidence. > 2) The radiology report (in RDF) asserts the presence of > microcalcifications and refers to the entire image as evidence, along > with a image processing/feature extraction program that will highlight > the phenomenon in the image. > 3) The radiology report (in RDF) asserts the presence of > microcalcifications and refers to a specific region in the image as > evidence using some function of a 2D coordinate system such as > polyline. > > The question: How can we refer to the microcalcifications as an > indication of a certain type of tumor in each case 1, 2, and 3 in RDF? > > I am especially interested in the 'structural' aspects: How do we > refer to the image document as containingEvidence ? How can we refer > to a *region* of the image in the document? How can we refer to the > software that will extract the relevant features with statistical > confidence, etc.? > > Any ideas or pointers to existing practices would be appreciated. I'm > aware of some related work in multimedia to refer to temporal regions > but I am specifically interested in spatial regions. > > Note that an analogous question of practice exists for textual > documents such as literature in PubMed that can be text-mined for > (evidence of) assertions. > > * Note: 2D is a simplification that should come in handy in > implementations and often deemed necessary, such as thumbnails. > > -Scott > > -- > M. Scott Marshall, W3C HCLS IG co-chair, http://www.w3.org/blog/hcls > Leiden University Medical Center / University of Amsterdam > http://staff.science.uva.nl/~marshall > > On Mon, Jan 10, 2011 at 4:01 PM, Tim Berners-Lee <timbl(a)w3.org> wrote: >> It is well to look at and make best practices for the things >> we have if we don't >> >> It was the FOAF folks who, initially, instead of using linked data, >> used an Inverse Functional Property to uniquely identify >> someone and then rdfs:seeAlso to find the data about them. >> So any FOAF browser has to look up the seeAlso or they >> don't follow any links. >> >> So tabulator always when looking up x and finding x see:also y will >> load y. So must any similar client or any crawler. >> >> So there is a lot of existing use we would throw away if we >> allowed rdfs:seeAlso for pointing to things which do not >> provide data. (It isn't the question of conneg or mime type, >> that is a red herring. it is whether there is machine-redable >> standards-based stuff about x). >> >> Further, we should not make any weaker properties like seeDocumentation >> subproperties of see:Also, or they would imply >> We maybe need a very weak top property like >> >> mayHaveSomeKindOfInfoAboutThis >> >> to be the superProperty of all the others. >> >> One things which could be stronger than seeAlso is definedBy if it >> is normally used for data, to point to the definitive ontology. >> That would then imply seeAlso. >> >> Tim > > -- --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 TaxonConcept Knowledge Base <http://www.taxonconcept.org/> / GeoSpecies Knowledge Base <http://lod.geospecies.org/> About the GeoSpecies Knowledge Base <http://about.geospecies.org/> ------------------------------------------------------------

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dcterms:creator
by Hannu Saarenmaa 14 Jan '11

14 Jan '11

Greetings We would need a term to store the name of the person who has digitised a sample. The current Darwin Core does not seem to include such term. Dublin Core's "creator" is what we'd use. I wonder why not all of the Dublin Core's 15 basic terms are included in Darwin Core terms web page, but just a subset of them, which subset seems to be somewhat random to me? We could also use the DC term "contributor" or something for someone who has proof-read the digitisation result. I understand that nothing breaks if we use dc:creator because the Dublin Core schema loads it along with other elements. But because of this omission some applications like GBIF IPT omit it from their mapping capabilities, which is a problem. Your advise is sppreaciated, Hannu -- Hannu Saarenmaa, Project Manager Digitisation Centre of the Finnish Museum of Natural History Faculty of Science and Forestry University of Eastern Finland P.O. Box 111 FIN-80101 Joensuu Street address: Länsikatu 15, room 2C113 in Joensuu Science Park hannu.saarenmaa(a)helsinki.fi Telephone +358-13-251-5705 Mobile +358-50-4479668

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