Establishing a distributed system for the simple representation and integration of diverse scientific assertions View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2010-06

AUTHORS

Matthias Samwald, Holger Stenzhorn

ABSTRACT

BACKGROUND: Information technology has the potential to increase the pace of scientific progress by helping researchers in formulating, publishing and finding information. There are numerous projects that employ ontologies and Semantic Web technologies towards this goal. However, the number of applications that have found widespread use among biomedical researchers is still surprisingly small. In this paper we present the aTag ('associative tags') convention, which aims to drastically lower the entry barriers to the biomedical Semantic Web. aTags are short snippets of HTML+RDFa with embedded RDF/OWL based on the Semantically Interlinked Online Communities (SIOC) vocabulary and domain ontologies and taxonomies, such as the Open Biomedical Ontologies and DBpedia. The structure of aTags is very simple: a short piece of human-readable text that is 'tagged' with relevant ontological entities. This paper describes our efforts for seeding the creation of a viable ecosystem of datasets, tools and services around aTags. RESULTS: Numerous biomedical datasets in aTag format and systems for the creation of aTags have been set-up and are described in this paper. Prototypes of some of these systems are accessible at http://hcls.deri.org/atag CONCLUSIONS: The aTags convention enables the rapid development of diverse, integrated datasets and semantically interoperable applications. More work needs to be done to study the practicability of this approach in different use-case scenarios, and to encourage uptake of the convention by other groups. More... »

PAGES

s5

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/2041-1480-1-s1-s5

DOI

http://dx.doi.org/10.1186/2041-1480-1-s1-s5

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1003383593

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/20626925


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0806", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Information Systems", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/08", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Information and Computing Sciences", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "name": [
            "Digital Enterprise Research Institute (DERI), Galway, Ireland"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Samwald", 
        "givenName": "Matthias", 
        "id": "sg:person.0661660735.59", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0661660735.59"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Digital Enterprise Research Institute (DERI), Galway, Ireland"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Stenzhorn", 
        "givenName": "Holger", 
        "id": "sg:person.01216110433.90", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01216110433.90"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1093/bioinformatics/bti1142", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013840461"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/gb-2005-6-5-r46", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015285227", 
          "https://doi.org/10.1186/gb-2005-6-5-r46"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.febslet.2008.02.070", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018697168"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt1346", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028001312", 
          "https://doi.org/10.1038/nbt1346"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-3-540-76298-0_52", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028565626", 
          "https://doi.org/10.1007/978-3-540-76298-0_52"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-3-540-76298-0_52", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028565626", 
          "https://doi.org/10.1007/978-3-540-76298-0_52"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btn117", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030142188"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ng.f.217", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035286240", 
          "https://doi.org/10.1038/ng.f.217"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-3-540-76298-0_40", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040218101", 
          "https://doi.org/10.1007/978-3-540-76298-0_40"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-3-540-76298-0_40", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040218101", 
          "https://doi.org/10.1007/978-3-540-76298-0_40"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btm557", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043760998"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-3-540-72216-8_21", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046468097", 
          "https://doi.org/10.1007/978-3-540-72216-8_21"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-3-540-72216-8_21", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046468097", 
          "https://doi.org/10.1007/978-3-540-72216-8_21"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bib/bbp004", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049086014"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bib/bbp004", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049086014"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.jbi.2008.04.010", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049175558"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1077808784", 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1077955348", 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1078353946", 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2010-06", 
    "datePublishedReg": "2010-06-01", 
    "description": "BACKGROUND: Information technology has the potential to increase the pace of scientific progress by helping researchers in formulating, publishing and finding information. There are numerous projects that employ ontologies and Semantic Web technologies towards this goal. However, the number of applications that have found widespread use among biomedical researchers is still surprisingly small. In this paper we present the aTag ('associative tags') convention, which aims to drastically lower the entry barriers to the biomedical Semantic Web. aTags are short snippets of HTML+RDFa with embedded RDF/OWL based on the Semantically Interlinked Online Communities (SIOC) vocabulary and domain ontologies and taxonomies, such as the Open Biomedical Ontologies and DBpedia. The structure of aTags is very simple: a short piece of human-readable text that is 'tagged' with relevant ontological entities. This paper describes our efforts for seeding the creation of a viable ecosystem of datasets, tools and services around aTags.\nRESULTS: Numerous biomedical datasets in aTag format and systems for the creation of aTags have been set-up and are described in this paper. Prototypes of some of these systems are accessible at http://hcls.deri.org/atag\nCONCLUSIONS: The aTags convention enables the rapid development of diverse, integrated datasets and semantically interoperable applications. More work needs to be done to study the practicability of this approach in different use-case scenarios, and to encourage uptake of the convention by other groups.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/2041-1480-1-s1-s5", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.3982754", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1043573", 
        "issn": [
          "2041-1480"
        ], 
        "name": "Journal of Biomedical Semantics", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "Suppl 1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "1"
      }
    ], 
    "name": "Establishing a distributed system for the simple representation and integration of diverse scientific assertions", 
    "pagination": "s5", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "101df4287a793e618572d4bfdb592019e52a9cf5c21c0b9704c8c4d4f39d09ad"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "20626925"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "101531992"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/2041-1480-1-s1-s5"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1003383593"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/2041-1480-1-s1-s5", 
      "https://app.dimensions.ai/details/publication/pub.1003383593"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T23:31", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8693_00000549.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1186%2F2041-1480-1-S1-S5"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/2041-1480-1-s1-s5'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/2041-1480-1-s1-s5'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/2041-1480-1-s1-s5'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/2041-1480-1-s1-s5'


 

This table displays all metadata directly associated to this object as RDF triples.

126 TRIPLES      21 PREDICATES      44 URIs      21 LITERALS      9 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/2041-1480-1-s1-s5 schema:about anzsrc-for:08
2 anzsrc-for:0806
3 schema:author N97c3f04944ca479297024a86d7b9d2c4
4 schema:citation sg:pub.10.1007/978-3-540-72216-8_21
5 sg:pub.10.1007/978-3-540-76298-0_40
6 sg:pub.10.1007/978-3-540-76298-0_52
7 sg:pub.10.1038/nbt1346
8 sg:pub.10.1038/ng.f.217
9 sg:pub.10.1186/gb-2005-6-5-r46
10 https://app.dimensions.ai/details/publication/pub.1077808784
11 https://app.dimensions.ai/details/publication/pub.1077955348
12 https://app.dimensions.ai/details/publication/pub.1078353946
13 https://doi.org/10.1016/j.febslet.2008.02.070
14 https://doi.org/10.1016/j.jbi.2008.04.010
15 https://doi.org/10.1093/bib/bbp004
16 https://doi.org/10.1093/bioinformatics/bti1142
17 https://doi.org/10.1093/bioinformatics/btm557
18 https://doi.org/10.1093/bioinformatics/btn117
19 schema:datePublished 2010-06
20 schema:datePublishedReg 2010-06-01
21 schema:description BACKGROUND: Information technology has the potential to increase the pace of scientific progress by helping researchers in formulating, publishing and finding information. There are numerous projects that employ ontologies and Semantic Web technologies towards this goal. However, the number of applications that have found widespread use among biomedical researchers is still surprisingly small. In this paper we present the aTag ('associative tags') convention, which aims to drastically lower the entry barriers to the biomedical Semantic Web. aTags are short snippets of HTML+RDFa with embedded RDF/OWL based on the Semantically Interlinked Online Communities (SIOC) vocabulary and domain ontologies and taxonomies, such as the Open Biomedical Ontologies and DBpedia. The structure of aTags is very simple: a short piece of human-readable text that is 'tagged' with relevant ontological entities. This paper describes our efforts for seeding the creation of a viable ecosystem of datasets, tools and services around aTags. RESULTS: Numerous biomedical datasets in aTag format and systems for the creation of aTags have been set-up and are described in this paper. Prototypes of some of these systems are accessible at http://hcls.deri.org/atag CONCLUSIONS: The aTags convention enables the rapid development of diverse, integrated datasets and semantically interoperable applications. More work needs to be done to study the practicability of this approach in different use-case scenarios, and to encourage uptake of the convention by other groups.
22 schema:genre research_article
23 schema:inLanguage en
24 schema:isAccessibleForFree true
25 schema:isPartOf N4552512ea6c2428a92efd7af13e228bd
26 N67fbc08cc5504b6280dbc95030b42767
27 sg:journal.1043573
28 schema:name Establishing a distributed system for the simple representation and integration of diverse scientific assertions
29 schema:pagination s5
30 schema:productId N72d15808dbdc41398f78c559a7010cc4
31 N7802b49c50f144a88b1aa0b992d001e2
32 N8b2936d393b1488cb017be63866576c5
33 Ndff400701d874e3499d87b66d3562254
34 Nf07b4543f6a9459cb70d4830cd7970ed
35 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003383593
36 https://doi.org/10.1186/2041-1480-1-s1-s5
37 schema:sdDatePublished 2019-04-10T23:31
38 schema:sdLicense https://scigraph.springernature.com/explorer/license/
39 schema:sdPublisher N9cd0cfda458a49f1b3e83398e0ec84cc
40 schema:url http://link.springer.com/10.1186%2F2041-1480-1-S1-S5
41 sgo:license sg:explorer/license/
42 sgo:sdDataset articles
43 rdf:type schema:ScholarlyArticle
44 N2359b4f731a646598ab34649f51e4258 rdf:first sg:person.01216110433.90
45 rdf:rest rdf:nil
46 N4552512ea6c2428a92efd7af13e228bd schema:issueNumber Suppl 1
47 rdf:type schema:PublicationIssue
48 N67fbc08cc5504b6280dbc95030b42767 schema:volumeNumber 1
49 rdf:type schema:PublicationVolume
50 N72d15808dbdc41398f78c559a7010cc4 schema:name nlm_unique_id
51 schema:value 101531992
52 rdf:type schema:PropertyValue
53 N7802b49c50f144a88b1aa0b992d001e2 schema:name dimensions_id
54 schema:value pub.1003383593
55 rdf:type schema:PropertyValue
56 N8b2936d393b1488cb017be63866576c5 schema:name doi
57 schema:value 10.1186/2041-1480-1-s1-s5
58 rdf:type schema:PropertyValue
59 N97c3f04944ca479297024a86d7b9d2c4 rdf:first sg:person.0661660735.59
60 rdf:rest N2359b4f731a646598ab34649f51e4258
61 N9cd0cfda458a49f1b3e83398e0ec84cc schema:name Springer Nature - SN SciGraph project
62 rdf:type schema:Organization
63 Nd48e609b6e904104a70edb0764469dda schema:name Digital Enterprise Research Institute (DERI), Galway, Ireland
64 rdf:type schema:Organization
65 Nde2952361cda4405936b8229c07404e9 schema:name Digital Enterprise Research Institute (DERI), Galway, Ireland
66 rdf:type schema:Organization
67 Ndff400701d874e3499d87b66d3562254 schema:name readcube_id
68 schema:value 101df4287a793e618572d4bfdb592019e52a9cf5c21c0b9704c8c4d4f39d09ad
69 rdf:type schema:PropertyValue
70 Nf07b4543f6a9459cb70d4830cd7970ed schema:name pubmed_id
71 schema:value 20626925
72 rdf:type schema:PropertyValue
73 anzsrc-for:08 schema:inDefinedTermSet anzsrc-for:
74 schema:name Information and Computing Sciences
75 rdf:type schema:DefinedTerm
76 anzsrc-for:0806 schema:inDefinedTermSet anzsrc-for:
77 schema:name Information Systems
78 rdf:type schema:DefinedTerm
79 sg:grant.3982754 http://pending.schema.org/fundedItem sg:pub.10.1186/2041-1480-1-s1-s5
80 rdf:type schema:MonetaryGrant
81 sg:journal.1043573 schema:issn 2041-1480
82 schema:name Journal of Biomedical Semantics
83 rdf:type schema:Periodical
84 sg:person.01216110433.90 schema:affiliation Nd48e609b6e904104a70edb0764469dda
85 schema:familyName Stenzhorn
86 schema:givenName Holger
87 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01216110433.90
88 rdf:type schema:Person
89 sg:person.0661660735.59 schema:affiliation Nde2952361cda4405936b8229c07404e9
90 schema:familyName Samwald
91 schema:givenName Matthias
92 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0661660735.59
93 rdf:type schema:Person
94 sg:pub.10.1007/978-3-540-72216-8_21 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046468097
95 https://doi.org/10.1007/978-3-540-72216-8_21
96 rdf:type schema:CreativeWork
97 sg:pub.10.1007/978-3-540-76298-0_40 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040218101
98 https://doi.org/10.1007/978-3-540-76298-0_40
99 rdf:type schema:CreativeWork
100 sg:pub.10.1007/978-3-540-76298-0_52 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028565626
101 https://doi.org/10.1007/978-3-540-76298-0_52
102 rdf:type schema:CreativeWork
103 sg:pub.10.1038/nbt1346 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028001312
104 https://doi.org/10.1038/nbt1346
105 rdf:type schema:CreativeWork
106 sg:pub.10.1038/ng.f.217 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035286240
107 https://doi.org/10.1038/ng.f.217
108 rdf:type schema:CreativeWork
109 sg:pub.10.1186/gb-2005-6-5-r46 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015285227
110 https://doi.org/10.1186/gb-2005-6-5-r46
111 rdf:type schema:CreativeWork
112 https://app.dimensions.ai/details/publication/pub.1077808784 schema:CreativeWork
113 https://app.dimensions.ai/details/publication/pub.1077955348 schema:CreativeWork
114 https://app.dimensions.ai/details/publication/pub.1078353946 schema:CreativeWork
115 https://doi.org/10.1016/j.febslet.2008.02.070 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018697168
116 rdf:type schema:CreativeWork
117 https://doi.org/10.1016/j.jbi.2008.04.010 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049175558
118 rdf:type schema:CreativeWork
119 https://doi.org/10.1093/bib/bbp004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049086014
120 rdf:type schema:CreativeWork
121 https://doi.org/10.1093/bioinformatics/bti1142 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013840461
122 rdf:type schema:CreativeWork
123 https://doi.org/10.1093/bioinformatics/btm557 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043760998
124 rdf:type schema:CreativeWork
125 https://doi.org/10.1093/bioinformatics/btn117 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030142188
126 rdf:type schema:CreativeWork
 




Preview window. Press ESC to close (or click here)


...