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Example

Following figure illustrates the annotations’ structure of SoMeSci on an example sentence containing a mention of the software “R”.

Description

Knowledge about software used in scientific investigations is important for several reasons, for instance, to enable an understanding of provenance and methods involved in data handling. However, software is usually not formally cited, but rather mentioned informally within the scholarly description of the investigation, raising the need for automatic information extraction and disambiguation. Given the lack of reliable ground truth data, we present SoMeSci - Software Mentions in Science - a gold standard knowledge graph of software mentions in scientific articles. It contains high quality annotations (IRR: κ = .82) of 3756 software mentions in 1367 PubMed Central articles. Besides the plain mention of the software, we also provide relation labels for additional information, such as the version, the developer, a URL or citations. Moreover, we distinguish between different types, such as application, plugin or programming environment, as well as different types of mentions, such as usage or creation. To the best of our knowledge, SoMeSci is the most comprehensive corpus about software mentions in scientific articles, providing training samples for Named Entity Recognition, Relation Extraction, Entity Disambiguation, and Entity Linking. Finally, we sketch potential use cases and provide baseline results for the different tasks.

Data model

The figure below displays the data model of SoMeSci.

Statistics

Feature Value
Triples 399,942
Resources 56,168
Distinct types 8
Distinct properties 45
Documents in “Creation Sentences” 110
Documents in “PLoS methods” 480
Documents in “PLoS sentences” 677
Documents in “Pubmed fulltexts” 100
Sentences 47,524
Entity mentions 7,237
Versions 1,381
Developers 858
Citations 588
URLs 347
Releases 87
Abbreviations 81
Licenses 53
Alternative names 35

Dataset

Dataset files

The latest release of SoMeSci can be downloaded at https://zenodo.org/record/4701763.

SPARQL endpoint

A SPARQL endpoint is available to send SPARQL queries and retrieve results from the SoMeSci knowledge graph.

https://data.gesis.org/somesci/sparql

Graph URL: http://data.gesis.org/somesci

Example 1: Requesting dataset metadata. (Result)

PREFIX dcterms: <http://purl.org/dc/terms/>

SELECT  ?p ?o ?p2 ?o2
WHERE{
    <http://data.gesis.org/somesci/> ?p ?o .
    OPTIONAL{
        ?s dcterms:creator ?o .
        ?o ?p2 ?o2
    }
}
ORDER BY ?p ?o ?p2 ?o2

Example 2: Requesting the number of documents per dataset. (Result)

PREFIX nif: <http://persistence.uni-leipzig.org/nlp2rdf/ontologies/nif-core#>
PREFIX void: <http://rdfs.org/ns/void#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX schema: <http://schema.org/>

SELECT ?datasetName (COUNT(?document) AS ?no_documents )
WHERE{
    ?document a nif:Context .
    ?document schema:isPartOf ?dataset .
    ?dataset dcterms:title ?datasetName .
}
GROUP BY ?datasetName
ORDER BY ?datasetName

Example 3: Requesting the top 10 of most mentioned software. (Result)

PREFIX nif: <http://persistence.uni-leipzig.org/nlp2rdf/ontologies/nif-core#>
PREFIX sms: <http://data.gesis.org/somesci/>
PREFIX its: <http://www.w3.org/2005/11/its/rdf#>

SELECT ?sw_identity (COUNT(?sw_identity) AS ?no_mentions)
WHERE{
    ?sw_phrase a nif:Phrase .
    ?sw_phrase its:taClassRef [rdfs:subClassOf sms:Software] .
    ?sw_phrase its:taIdentRef ?sw_identity .
}
ORDER BY DESC (?no_mentions) ?sw_identity
LIMIT 10

Example 4: Requesting spelling variations and alternative names of software. (Result)

PREFIX nif: <http://persistence.uni-leipzig.org/nlp2rdf/ontologies/nif-core#>
PREFIX sms: <http://data.gesis.org/somesci/>
PREFIX its: <http://www.w3.org/2005/11/its/rdf#>

SELECT ?sw_identity (COUNT(DISTINCT ?spelling) AS ?no_spellings) (GROUP_CONCAT(DISTINCT ?spelling; SEPARATOR=", ") AS ?spelling_variations) (GROUP_CONCAT(DISTINCT ?alt_name; SEPARATOR=", ") AS ?alternative_names)
WHERE{
    ?sw_phrase a nif:Phrase .
    ?sw_phrase its:taClassRef [ rdfs:subClassOf sms:Software ] .
    ?sw_phrase its:taIdentRef ?sw_identity .
    ?sw_phrase nif:anchorOf ?spelling .
    OPTIONAL{
        ?sw_phrase sms:referredToBy ?alt_name_mention .
        ?alt_name_mention its:taClassRef [ rdfs:subClassOf sms:Software ] .
        ?alt_name_mention nif:anchorOf ?alt_name.
    }
}
GROUP BY ?sw_identity
ORDER BY DESC(?no_spellings) ?sw_identity

Example 5: Requesting citation completeness. (Result)

PREFIX nif: <http://persistence.uni-leipzig.org/nlp2rdf/ontologies/nif-core#>
PREFIX sms: <http://data.gesis.org/somesci/>
PREFIX its: <http://www.w3.org/2005/11/its/rdf#>

SELECT ?sw_type (COUNT(?sw_type) AS ?total) (COUNT(?version_phrase) AS ?no_versions) (COUNT(?url_phrase) AS ?no_urls) (COUNT(?citation_phrase) AS ?no_citations) (COUNT(?release_phrase) AS ?no_releases)
WHERE{
    ?sw_phrase its:taClassRef ?sw_type .
    OPTIONAL{
        ?sw_phrase sms:referredToByVersion ?version_phrase .
        ?version_phrase its:taClassRef sms:Version
    }
    OPTIONAL{
        ?sw_phrase sms:referredToByURL ?url_phrase .
        ?url_phrase its:taClassRef sms:URL
    }
    OPTIONAL{
        ?sw_phrase sms:referredToByCitation ?citation_phrase.
        ?citation_phrase its:taClassRef sms:Citation
    }
    OPTIONAL{
        ?sw_phrase sms:referredToByRelease ?release_phrase .
        ?release_phrase its:taClassRef sms:Release
    }
    VALUES ?sw_type {sms:ProgrammingEnvironment sms:Application sms:OperatingSystem sms:PlugIn }
}
GROUP BY ?sw_type
ORDER BY ?sw_type

Example 6: Requesting co-applied software. (Result)

PREFIX nif: <http://persistence.uni-leipzig.org/nlp2rdf/ontologies/nif-core#>
PREFIX sms: <http://data.gesis.org/somesci/>
PREFIX its: <http://www.w3.org/2005/11/its/rdf#>

SELECT (?ident_a AS ?sw) (GROUP_CONCAT(DISTINCT ?spelling_b; SEPARATOR=", " ) AS ?cooccurring_sw)
WHERE{
    ?sw_phrase_a a nif:Phrase .
    ?sw_phrase_a its:taClassRef [rdfs:subClassOf sms:Software] .
    ?sw_phrase_a its:taIdentRef ?ident_a .
    ?sw_phrase_a nif:referenceContext [nif:broaderContext ?common_broader_context] .
    ?sw_phrase_a nif:anchorOf ?spelling_a .

    ?sw_phrase_b a nif:Phrase .
    ?sw_phrase_b its:taClassRef [rdfs:subClassOf sms:Software] .
    ?sw_phrase_b its:taIdentRef ?ident_b .
    ?sw_phrase_b nif:referenceContext [nif:broaderContext ?common_broader_context] .
    ?sw_phrase_b nif:anchorOf ?spelling_b .

    FILTER( STRLEN (?spelling_b) < 25 )
    FILTER(?ident_a != ?ident_b)
}
GROUP BY ?ident_a
ORDER BY ?ident_a

Example 7: Requesting number of sentences by number of annotations. (Result)

PREFIX nif: <http://persistence.uni-leipzig.org/nlp2rdf/ontologies/nif-core#>
PREFIX its: <http://www.w3.org/2005/11/its/rdf#>

SELECT ?no_labels (COUNT(?sentence) AS ?no_sentences)
WHERE{
    SELECT ?sentence (COUNT(?annotation_phrase) AS ?no_labels)
    WHERE{
        ?sentence a nif:Sentence .
        OPTIONAL{
            ?annotation_phrase nif:referenceContext ?sentence .
        }
    }
    GROUP BY ?sentence
}
GROUP BY ?no_labels
ORDER BY ?no_labels

Source code

The source code of all components of SoMeSci is available on GitHub at https://github.com/dave-s477/SoMeSci_Code.

License

The dataset is published under a Creative Commons Attribution 4.0 license.

Publications

David Schindler, Felix Bensmann, Stefan Dietze, and Frank Krüger. 2021. SoMeSci - A 5 Star Open Data Gold Standard Knowledge Graph of Software Mentions in Scientific Articles. In Proceedings of the 30th ACM International Conference on Information & Knowledge Management (CIKM ‘21). Association for Computing Machinery, New York, NY, USA, 4574–4583. DOI: https://doi.org/10.1145/3459637.3482017

Contact

Please provide your feedback and any comments by sending an email to somesci (at) gesis (dot) org .

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