[CF-metadata] Extensions to the Standard Name table

Leadbetter, Adam alead at bodc.ac.uk
Mon Nov 12 07:39:31 MST 2012


Dear all

Just to update you - I've gained a little more understanding of SPARQL and have an update to the query B from my earlier e-mail (below) which gives (for example) the following results:

standardName	                                                                                           pollutant	       source
"surface_upward_mass_flux_of_carbon_dioxide_expressed_as_carbon_due_to_emission_from_crop_harvesting" @en    "Carbon dioxide"  "harvest"

Thanks

Adam

--Query B (updated)
PREFIX skos:<http://www.w3.org/2004/02/skos/core#>
PREFIX j.0: <http://rdfdata.eionet.europa.eu/airbase/schema/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?standardName ?pollutant ?source WHERE
{
  BIND("surface_upward_mass_flux_of_carbon_dioxide_expressed_as_carbon_due_to_emission_from_crop_harvesting" AS ?stdname)
  {SELECT ?standardName ?urisn ?urip ?urig ?source WHERE
  {
    <http://vocab.nerc.ac.uk/collection/P07/current/> skos:member ?urisn.
    ?urisn skos:prefLabel ?standardName.
    ?urisn skos:broader ?urip
    FILTER CONTAINS (str(?urip),"eionet").
    OPTIONAL
    {
      ?urisn skos:related ?urig
      FILTER CONTAINS (str(?urig),"gemet")
    }
  }} FILTER (str(?standardName) = str(?stdname))
  SERVICE <http://cr.eionet.europa.eu/sparql>
  {
    ?urie j.0:pollutant ?pollutant
    FILTER (?urie=?urip).
    ?urige rdfs:label ?source
    FILTER (?urige=?urig)
  }
}


-----Original Message-----
From: CF-metadata [mailto:cf-metadata-bounces at cgd.ucar.edu] On Behalf Of Leadbetter, Adam
Sent: 29 October 2012 13:33
To: Schultz, Martin; cf-metadata at cgd.ucar.edu
Subject: Re: [CF-metadata] Extensions to the Standard Name table

Dear Martin and all

I've done some mappings between the CF Standard Names at http://vocab.nerc.ac.uk/collection/P07/ and both the EEA Atmospheric Pollutants vocabulary and GEMET. The mapped Standard Names can be found by running Query 'A' below in http://vocab.nerc.ac.uk/sparql/. I've tried, and failed, to get a decent response time from the federated query (I'm still learning SPARQL so it's likely I'm doing something wrong) but I have attached a Query B which shows you the mappings to the EEA pollutant name & the mappings to GEMET for a given Standard Name. It can be a bit slow, so you may need to show it some patience.

If anyone knows SPARQL better than I do, and can do improve Query B then please feel free to do so.

This is currently implemented as a "proof of concept" using some loose mappings, and it may be that you have suggestions on better terms to map to. If this the sort of thing you wanted and is of use to the CF community we can certainly expand the number of mappings done but we could also investigate firming up the mappings using more specific relationships.

Let me know what you think

Thanks

Adam



--Query A

PREFIX skos:<http://www.w3.org/2004/02/skos/core#>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
SELECT DISTINCT ?standardName WHERE
{
  <http://vocab.nerc.ac.uk/collection/P07/current/> rdf:type skos:Collection.
  <http://vocab.nerc.ac.uk/collection/P07/current/> skos:member ?uri.
  ?uri  skos:prefLabel ?standardName.
  ?uri  ?relationship ?eionet
  FILTER CONTAINS (str(?eionet),'eionet') }




--Query B

PREFIX skos:<http://www.w3.org/2004/02/skos/core#>
PREFIX j.0: <http://rdfdata.eionet.europa.eu/airbase/schema/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?standardName ?pollutant ?urig WHERE {
  BIND("surface_upward_mass_flux_of_carbon_dioxide_expressed_as_carbon_due_to_emission_from_crop_harvesting" AS ?stdname)
  {SELECT ?standardName ?urisn ?urip ?urig WHERE
  {
    <http://vocab.nerc.ac.uk/collection/P07/current/> skos:member ?urisn.
    ?urisn skos:prefLabel ?standardName.
    ?urisn skos:broader ?urip
    FILTER CONTAINS (str(?urip),"eionet").
    OPTIONAL
    {
      ?urisn skos:related ?urig
      FILTER CONTAINS (str(?urig),"gemet")
    }
  }} FILTER (str(?standardName) = str(?stdname))
  SERVICE <http://cr.eionet.europa.eu/sparql>
  {
    ?urip j.0:pollutant ?pollutant.
  }
}


____________________________________________________________
Dr. Adam Leadbetter

Data Scientist
British Oceanographic Data Centre
Joseph Proudman Building
6 Brownlow Street
Liverpool
L3 5DA

Tel: 0151 795 4878

-----Original Message-----
From: Schultz, Martin [mailto:m.schultz at fz-juelich.de]
Sent: 22 October 2012 15:07
To: Leadbetter, Adam; Lowry, Roy K.; cf-metadata at cgd.ucar.edu
Subject: AW: [CF-metadata] Extensions to the Standard Name table

Great! Looking forward to test this!

Cheers,

Martin

-----Ursprüngliche Nachricht-----
Von: Leadbetter, Adam [mailto:alead at bodc.ac.uk]
Gesendet: Montag, 22. Oktober 2012 14:45
An: Lowry, Roy K.; Schultz, Martin; cf-metadata at cgd.ucar.edu
Betreff: RE: [CF-metadata] Extensions to the Standard Name table

Hi Martin

I'll aim to have the small demonstrator with mappings in place towards the end of this week, or early next week.

Thanks

Adam
________________________________________
From: Lowry, Roy K.
Sent: 21 October 2012 17:17
To: Schultz, Martin; cf-metadata at cgd.ucar.edu
Cc: Leadbetter, Adam
Subject: RE: [CF-metadata] Extensions to the Standard Name table

OK Martin,

I'm on leave for the next 2 weeks, but will try and get a demonstration mapping with 4 or 5 contaminants mapped the week after I get back (unless Adam can do something in the mean time).

Cheers, Roy.

________________________________
From: Schultz, Martin [m.schultz at fz-juelich.de]
Sent: 21 October 2012 15:00
To: Lowry, Roy K.; cf-metadata at cgd.ucar.edu
Cc: Leadbetter, Adam
Subject: AW: [CF-metadata] Extensions to the Standard Name table

Hello Roy,

     this sounds indeed convincing. If there is indeed some funding to establish this by January, and if we can then somehow ensure continuity (someone would have to update the mapping whenever there are changes to the standard_name table, and we should be in a position to add more rows to the table even after funding will have ended), then this sounds like a good plan.

Cheers,

Martin


Von: Lowry, Roy K. [mailto:rkl at bodc.ac.uk]
Gesendet: Sonntag, 21. Oktober 2012 10:21
An: Schultz, Martin; cf-metadata at cgd.ucar.edu
Cc: Leadbetter, Adam
Betreff: RE: [CF-metadata] Extensions to the Standard Name table

Hello Marin,

I'm not sure what would be possible using the string-matching SPARQL approach. It would be perfectly possible to do that from a relational database using SQL (which I do know) and so it may be possible.  I'll see if Adam can come up with anything (I've yet to learn the language).

However, I am certain that if we installed a mapping (maybe a day's work) then it could be done - all the query would have to do is identify whether or not there is a mapping from the Standard Name reference to the EEA vocabulary and match on it if it exists.

Installing a mapping in NVS fulfils exactly the same function as adding a link to the Standard Name table.  The difference is that the former process simply involves population of operational technological infrastructure (a mapping is a row in an Oracle table) with some funding support if the work is done before the end of January, whereas the latter would require infrastructure development in addition to population.

Cheers, Roy.

________________________________
From: CF-metadata [cf-metadata-bounces at cgd.ucar.edu] On Behalf Of Schultz, Martin [m.schultz at fz-juelich.de]
Sent: 20 October 2012 11:43
To: cf-metadata at cgd.ucar.edu<mailto:cf-metadata at cgd.ucar.edu>
Subject: Re: [CF-metadata] Extensions to the Standard Name table Dear Roy,

     thanks a lot for this nice example of true interoperability. Yet, two questions remain: 1) what I would be even more interested in is the inverse problem, i.e. given a standard_name, I would like to know which compound it contains. 2) I expect that this is more difficult, in particular if we don't know a priori that the given standard_name does contain a compound name. Generally, this is where I see the difficulty with your brokered approach: how do you find out which controlled vocabulary list(s) have to be applied in order to identify the components of a standard_name? Think of "tendency_of_X_due_to_emissions_from_Y" where you want to link both the compound and the emission sector to the respecitve controlled vocabulary table. Then, in another standard_name you will find some marine bacteria or so which relate to yet another vocabulary list, and so on. Unless I miss the point here, I would still argue that it will be more efficient and less ambiguous if the link would be provided in the standard_name table itself.

What do you think?

Cheers,

Martin




Date: Fri, 19 Oct 2012 12:30:42 +0100

From: "Lowry, Roy K." <rkl at bodc.ac.uk<mailto:rkl at bodc.ac.uk>>

To: "cf-metadata at cgd.ucar.edu<mailto:cf-metadata at cgd.ucar.edu>" <cf-metadata at cgd.ucar.edu<mailto:cf-metadata at cgd.ucar.edu>>

Subject: [CF-metadata] Extensions to the Standard Name table

Message-ID:

                <40829B0E077C1145A6DE44D39B3830A921F5722C84 at nerckwmb1.ad.nerc.ac.uk<mailto:40829B0E077C1145A6DE44D39B3830A921F5722C84 at nerckwmb1.ad.nerc.ac.uk>>

Content-Type: text/plain; charset="us-ascii"



Dear All,



Martin Schultz was proposing an extension to the Standard Name table to provide a means of easily identifying the Standard Names associated with a given atmospheric contaminant.  What follows provides an alternative way to address his use case.  Go to the URL http://vocab.nerc.ac.uk/sparql/ and copy the SPARQL query at the end of this message into the box, choose your output format and press 'Get Results'. If you don't want 'carbon monoxide' simply replace 'Carbon monoxide' by another valid EEA contaminant name.



For the techies on the list, this is done by a federated SPARQL query involving SPARQL endpoints on vocabulary servers at BODC and the EEA. This is based on string matching, but could be made more robust by implementing an EEA/Standard Names mapping in NVS should this be requested by the CF community.



Cheers, Roy.





PREFIX skos: <http://www.w3.org/2004/02/skos/core#<http://www.w3.org/2004/02/skos/core>>

PREFIX j.0: <http://rdfdata.eionet.europa.eu/airbase/schema/>

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#<http://www.w3.org/2000/01/rdf-schema>>

SELECT ?urie ?labele ?urin ?labeln WHERE {

  BIND("Carbon monoxide" AS ?pollutant)

  	.

  <http://vocab.nerc.ac.uk/collection/P07/current/> skos:member ?urin.

  ?urin skos:prefLabel ?labeln.

  ?urin skos:definition ?defn.

  FILTER CONTAINS (str(lcase(?defn)),str(lcase(?pollutant)))

}





PD Dr. Martin G. Schultz
IEK-8, Forschungszentrum Jülich
D-52425 Jülich
Ph: +49 2461 61 2831



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