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AMR-LD (AMRs as Linked Data)

Advantages of AMR-LD

  • Sharable in standard W3C format

  • Some reasoning for free (using RDF/OWL tools):

    • amr:ARG0-of owl:inverseOf amr:ARG0
    • inheritance reasoning:
      If :p rdf:type amr-ne:enzyme .
     ame-ne:enzyme rdfs:subClassOf amr-ne:protein .
  Then :p rdf:type amr-ne:protein

  • Linked to well know identifiers/entities

      :e amr:xref up:RASH_HUMAN .
  :e amr:xref pfam:PF00071 .

  • Making semantic assertions of precise equivalence using owl:sameAs relations

      :e owl:sameAs up:RASH_HUMAN .

  • Query tools for free (SPARQL)

    • Names of proteins in a AMR repository
      select ?n
  where  { ?p rdf:type amr-ne:protein .
       ?p amr:name ?no .
     ?no rdf:type amr-ne:name .
     ?no :op1 ?n }
    • All propbank events (verbs) that have a protein as :ARG1
      select ?v
  where { ?e rdf:type ?v .
        ?e amr:ARG1 ?p .
     ?p rdf:type amr-ne:protein .
     ### we would get all the "amr-ne:enzyme"s if reasoning enabled
     }
    • All propbank events (verbs) that have a protein as :ARG*
      select ?v
  where { ?e rdf:type ?v .
        ?e ?arg ?p .
     ?p rdf:type amr-ne:protein .
     ### we would get all the "amr-ne:enzyme"s if reasoning enabled
     FILTER regex(?arg, "ARG", "i") }
     }

2. AMR-LD example

The cjconsensus Gold-Standard data set contains the following AMR (from a sentence in the results section of Innocenti et al. 2002):

# ::id pmid_1177_7939.53 ::date 2015-03-07T10:57:15 ::annotator SDL-AMR-09 ::preferred
# ::snt Sos-1 has been shown to be part of a signaling complex with Grb2, which mediates the activation of Ras upon RTK stimulation.
# ::save-date Fri Mar 13, 2015 ::file pmid_1177_7939_53.txt
(s / show-01
      :ARG1 (h / have-part-91
            :ARG1 (m / macro-molecular-complex
                  :ARG0-of (s2 / signal-07)
                  :part (p2 / protein :name (n2 / name :op1 "Grb2")
                        :ARG0-of (m2 / mediate-01
                              :ARG1 (a / activate-01
                                    :ARG1 (e / enzyme :name (n3 / name :op1 "Ras"))
                                    :condition (s3 / stimulate-01
                                          :ARG1 (e2 / enzyme :name (n4 / name :op1 "RTK")))))))
            :ARG2 (p / protein :name (n / name :op1 "Sos-1"))))

Under our current rubric, this would then be translated to the following RDF TTL code, with a fairly simple one-to-one mapping from AMR elements to RDF elements.

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>.
@prefix xsd: <http://www.w3.org/2001/XMLSchema#>.

@prefix amr: <http://amr.isi.edu#>
@prefix pb: <https://verbs.colorado.edu/propbank#>
@prefix ontonotes: <https://catalog.ldc.upenn.edu/LDC2013T19#>
@prefix amr-ne: <http://amr.isi.edu/entity-types#>

@prefix up: <http://www.uniprot.org/uniprot/>
@prefix pfam: <http://pfam.xfam.org/family/>


### : is the default namespace

:a1 rdf:type amr:AMR .
:a1 amr:has-sentence "Sos-1 has been shown to be part of a signaling complex with Grb2, which mediates the activation of Ras upon RTK stimulation." .
:a1 amr:has-id "pmid_1177_7939.53"
:a1 amr:has-date "2015-03-07T10:57:15
:a1 amr:has-annotator SDL-AMR-09
:a1 amr:is-preferred "true"^^xsd:boolean
:a1 amr:has-file "pmid_1177_7939_53.txt"

:a1 amr:has-root :s .   ### or :a1 amr:has-root :pmid_1177_7939.53__s
:s rdf:type pb:show-01 .
:s amr:ARG1 :h .
:h rdf:type pb:have-part-91 .
:h amr:ARG1 :m .
:m rdf:type amr-ne:macro-molecular-complex .
:m amr:ARG0-of :s2 .
:s2 rdf:type pb:signal-07 .
:m amr:part :p2 .
:p2 rdf:type amr-ne:protein .
:p2 :name :n2 .
:n2 rdf:type amr-ne:name .
:n2 amr:op1 "Grb2" .
:p2 amr:xref up:P62993 .
:p2 amr:xref up:GRB2_HUMAN .
:p2 amr:ARG0-of :m2 .
:m2 rdf:type pb:mediate-01 .
:m2 amr:ARG1 :a .
:a rdf:type pb:activate-01 .
:a amr:ARG1 :e .
:e rdf:type amr-ne:enzyme .
:e :name :n3 .
:n3 rdf:type amr-ne:name .
:n3 :op1 "Ras" .
:e amr:xref up:RASH_HUMAN .     ### we could also do:   :e owl:sameAs up:RASH_HUMAN  
:e amr:xref pfam:PF00071 .
:a amr:condition :s3 .
:s3 rdf:type pb:stimulate-01 .
:s3 amr:ARG1 :e2 .
:e2 rdf:type amr-ne:enzyme .
:e2 amr:name :n4 .
:n4 rdf:type amr-ne:name .
:n4 :op1 "RTK" .
:e2 amr:xref pfam:PF07714
:h amr:ARG2 :p .
:p rdf:type amr-ne:protein .
:p amr:name :n .
:n rdf:type amr:name .
:n :op1 "Sos-1" .

amr_to_rdf.py

This is a simple script that reads the AMR using libraries from the AMRICA toolkit and then transposes the graph structure of the AMR into RDF using rdflib. We use simple heuristics to map namespaces and to generate valid RDF for the AMR as needed.

How to run the script:

$ python amr_to_rdf.py -i <input AMR file> -o <output RDF file> [-f <format>]

How to test the script:

$ python amr_to_rdf.py -i test/bio_ras_0001_1.txt -o out.rdf -f nt