dbpedia, RDF and SPARQL – for chemistry

A comment on the last post

Richard Cyganiak Says: May 19th, 2007 at 7:55 pm e
Thanks for this nice introduction Peter. Note that the DBpedia URIs also work in a web browser, so you can go to http://dbpedia.org/resource/Uppsala and the DBpedia server will generate a web page showing the information it has about the item.

I have been playing some more with dbpedia and RDF. (It is important to realise that – as in the above example – many of the accesses will be through UIs, not raw RDF, so casual readers shouldn’t worry). There have been several ways of expressing RDF and these are slightly confusing but the important thing is to know what the predicates and potential values are. The exploratory approach (using a browser) Richard suggests is useful.
Let’s look at chemistry. Assume we know every little about dbpedia but we’ll look at some chemistry. So access Arsenic in Wikipedia


From Wikipedia, the free encyclopedia

33 germaniumarsenicselenium


Name, Symbol, Number arsenic, As, 33
Chemical series metalloids
Group, Period, Block 15, 4, p
Appearance metallic gray
Standard atomic weight 74.92160(2)  g·mol−1
Electron configuration [Ar] 3d10 4s2 4p3
Electrons per shell 2, 8, 18, 5
Physical properties
Phase solid
Density (near r.t.) 5.727  g·cm−3
Liquid density at m.p. 5.22  g·cm−3
Melting point 1090 K
(817 °C, 1503 °F)
Boiling point subl. 887 K
(614 °C, 1137 °F)
Critical temperature 1673 K
Heat of fusion (gray) 24.44  kJ·mol−1
Heat of vaporization ? 34.76  kJ·mol−1
Heat capacity (25 °C) 24.64  J·mol−1·K−1
P(Pa) 1 10 100 1 k 10 k 100 k
Atomic properties
Crystal structure rhombohedral
Oxidation states ±3, 5
(mildly acidic oxide)
Electronegativity 2.18 (Pauling scale)
Ionization energies
1st:  947.0  kJ·mol−1
2nd:  1798  kJ·mol−1
3rd:  2735  kJ·mol−1
Atomic radius 115pm
Atomic radius (calc.) 114  pm
Covalent radius 119  pm
Van der Waals radius 185 pm
Magnetic ordering no data
Electrical resistivity (20 °C) 333 n Ω·m
Thermal conductivity (300 K) 50.2  W·m−1·K−1
Young’s modulus 8  GPa
Bulk modulus 22  GPa
Mohs hardness 3.5
Brinell hardness 1440  MPa
CAS registry number 7440-38-2
Selected isotopes
iso NA half-life DM DE (MeV) DP
73As syn 80.3 d ε 73Ge
γ 0.05D, 0.01D, e
74As syn 17.78 d ε 74Ge
β+ 0.941 74Ge
γ 0.595, 0.634
β 1.35, 0.717 74Se
75As 100% As is stable with 42 neutrons

Arsenic (IPA: /ˈɑːsənɪk/, /ˈɑɹsənɪk/) is a chemical element that has the symbol As and atomic number 33. Its Atomic Mass is 74.92. Its Ionic Charge is (3-) Its position in the periodic table is shown at right. This is a notoriously poisonous metalloid that has many allotropic forms: yellow (molecular non-metallic) and several black and gray forms (metalloids) are a few that are seen. Three metalloidal forms of arsenic with different crystal structures are found free in nature (the minerals arsenic sensu strictu and the much rarer arsenolamprite and pararsenolamprite), but it is more commonly found as arsenide and arsenate compounds. Several hundred such mineral species are known. Arsenic and its compounds are used as pesticides, herbicides, insecticides and various alloys.

The box on the right is the “infobox” and it is many of these properties that find their way into dbpedia. The property names are not yet fully standardised and not all are memorable, but Wikipedian chemists can – and I suspect will – work on these to stnadrdaize. In which case they can be used for RDF/SPARQL queries. For example:
[… white space inserted for formatting – scroll down …]

  As http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://dbpedia.org/resource/Category:Chemical_elements
  As http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://dbpedia.org/resource/Category:Toxicology
  As http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://dbpedia.org/resource/Category:Metalloids
  As http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://dbpedia.org/resource/Category:Pnictogens
  As http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://dbpedia.org/resource/Category:Arsenic
  As http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://dbpedia.org/class/yago/chemical_element
  As http://www.w3.org/2004/02/skos/core#subject http://dbpedia.org/resource/Category:Articles_with_unsourced_statements
  As http://www.w3.org/2004/02/skos/core#subject http://dbpedia.org/resource/Category:Chemical_elements
  As http://www.w3.org/2004/02/skos/core#subject http://dbpedia.org/resource/Category:Toxicology
  As http://www.w3.org/2004/02/skos/core#subject http://dbpedia.org/resource/Category:Metalloids
  As http://www.w3.org/2004/02/skos/core#subject http://dbpedia.org/resource/Category:Pnictogens
  As http://www.w3.org/2004/02/skos/core#subject http://dbpedia.org/resource/Category:Arsenic
  As http://dbpedia.org/property/reference http://www.asmalldoseof.org/
  As http://dbpedia.org/property/reference http://www.atsdr.cdc.gov/HEC/CSEM/arsenic/
  As http://dbpedia.org/property/reference http://www.clu-in.org/contaminantfocus/default.focus/sec/arsenic/cat/Overview/
  As http://dbpedia.org/property/reference http://www-cie.iarc.fr/htdocs/monographs/vol23/arsenic.html
  As http://dbpedia.org/property/reference http://www.greenfacts.org/arsenic/arsenic-1.htm
  As http://dbpedia.org/property/reference http://www.inchem.org/documents/ehc/ehc/ehc224.htm
  As http://dbpedia.org/property/reference http://www.npi.gov.au/database/substance-info/profiles/11.html
  As http://dbpedia.org/property/reference http://www.webelements.com/webelements/elements/text/As/index.html
  As http://dbpedia.org/property/reference http://www.origen.net/arsenic.html
  As http://www.w3.org/2000/01/rdf-schema#label Arsenic
  As http://www.w3.org/2000/01/rdf-schema#label Arsen
  As http://www.w3.org/2000/01/rdf-schema#label Ars\u00E9nico\”
  As http://www.w3.org/2000/01/rdf-schema#label Arsenic
  As http://www.w3.org/2000/01/rdf-schema#label Arsenico
  As http://www.w3.org/2000/01/rdf-schema#label \u30D2\u7D20\”
  As http://www.w3.org/2000/01/rdf-schema#label Arsenicum
  As http://www.w3.org/2000/01/rdf-schema#label Arsen
  As http://www.w3.org/2000/01/rdf-schema#label Ars\u00EAnio\”
  As http://www.w3.org/2000/01/rdf-schema#label Arsenik
  As http://www.w3.org/2000/01/rdf-schema#label \u7837\”
  As http://dbpedia.org/property/number 33
  As http://dbpedia.org/property/symbol As
  As http://dbpedia.org/property/left http://dbpedia.org/resource/germanium
  As http://dbpedia.org/property/right http://dbpedia.org/resource/selenium
  As http://dbpedia.org/property/above http://dbpedia.org/resource/phosphorus
  As http://dbpedia.org/property/below http://dbpedia.org/resource/antimony
  As http://dbpedia.org/property/color1 #cccc99
  As http://dbpedia.org/property/color2 black
  As http://dbpedia.org/property/group 15
  As http://dbpedia.org/property/period 4
  As http://dbpedia.org/property/block p
  As http://dbpedia.org/property/k [[sublimation (physics)|subl.]] 887
  As http://dbpedia.org/property/k 1090
  As http://dbpedia.org/property/c 614
  As http://dbpedia.org/property/c 817
  As http://dbpedia.org/property/f 1137
  As http://dbpedia.org/property/f 1503
  As http://dbpedia.org/property/mn 73
  As http://dbpedia.org/property/mn 74
  As http://dbpedia.org/property/mn 75
  As http://dbpedia.org/property/sym As
  As http://dbpedia.org/property/na 100
  As http://dbpedia.org/property/na http://dbpedia.org/resource/synthetic_radioisotope
  As http://dbpedia.org/property/n 42
  As http://dbpedia.org/property/hl [[1 E6 s|17.78]] d
  As http://dbpedia.org/property/hl [[1 E6 s|80.3]] [[day|d]]
  As http://dbpedia.org/property/dm1 \u03B5
  As http://dbpedia.org/property/dm1 http://dbpedia.org/resource/electron_capture
  As http://dbpedia.org/property/de1
  As http://dbpedia.org/property/pn1 73
  As http://dbpedia.org/property/pn1 74
  As http://dbpedia.org/property/ps1 http://dbpedia.org/resource/germanium
  As http://dbpedia.org/property/dm2 http://dbpedia.org/resource/Positron_emission
  As http://dbpedia.org/property/dm2 http://dbpedia.org/resource/Gamma_radiation
  As http://dbpedia.org/property/ps2
  As http://dbpedia.org/property/ps2 http://dbpedia.org/resource/germanium
  As http://dbpedia.org/property/de2 0.05[[Delayed nuclear radiation|D]], 0.01D, [[Conversion electron|e]]
  As http://dbpedia.org/property/de2 0.941
  As http://dbpedia.org/property/pn2 74
  As http://dbpedia.org/property/dm3 \u03B3
  As http://dbpedia.org/property/de3 0.595, 0.634

You can work out some of the property names by comparing against their values. For example…

http://dbpedia.org/resource/Arsenic As http://dbpedia.org/property/c

links to the melting point in degC. There is still some work to be done (e.g. linking properties and units) but RDF is well suited for this and we’ll be working out some approaches.

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3 Responses to dbpedia, RDF and SPARQL – for chemistry

  1. hello,
    I might be mistaken, but I am unable to properly view both the rdf triples table and the arsenic properties table (they overlap). I experience this both with firefox and IE 6.0.2.
    Thanks for your very interesting posts 🙂

  2. pm286 says:

    (1)Sorry – this is a problem with WordPress. I will try to add some space

  3. pm286 says:

    (2) should be better now. Possibly useful to have small type

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