Lost in Translation: Data Integration Tools Meet the Semantic Web (Experiences from the Ondex Project) View Full Text


Ontology type: schema:Chapter      Open Access: True


Chapter Info

DATE

2012

AUTHORS

Andrea Splendiani , Chris J. Rawlings , Shao-Chih Kuo , Robert Stevens , Phillip Lord

ABSTRACT

More information is now being published in machine processable form on the web and, as de-facto distributed knowledge bases are materializing, partly encouraged by the vision of the Semantic Web, the focus is shifting from the publication of this information to its consumption. Platforms for data integration, visualization and analysis that are based on a graph representation of information appear first candidates to be consumers of web-based information that is readily expressible as graphs. The question is whether the adoption of these platforms to information available on the Semantic Web requires some adaptation of their data structures and semantics. Ondex is a network-based data integration, analysis and visualization platform which has been developed in a Life Sciences context. A number of features, including semantic annotation via ontologies and an attention to provenance and evidence, make this an ideal candidate to consume Semantic Web information, as well as a prototype for the application of network analysis tools in this context. By analyzing the Ondex data structure and its usage, we have found a set of discrepancies and errors arising from the semantic mismatch between a procedural approach to network analysis and the implications of a web-based representation of information.We report in the paper on the simple methodology that we have adopted to conduct such analysis, and on issues that we have found which may be relevant for a range of similar platforms. More... »

PAGES

87-97

Book

TITLE

Recent Progress in Data Engineering and Internet Technology

ISBN

978-3-642-28797-8
978-3-642-28798-5

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-3-642-28798-5_13

DOI

http://dx.doi.org/10.1007/978-3-642-28798-5_13

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1038074257


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": {
          "alternateName": "Rothamsted Research", 
          "id": "https://www.grid.ac/institutes/grid.418374.d", 
          "name": [
            "Biomathematics and Bioinformatics Dept., Rothamsted Research, Harpenden, United Kingdom"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Splendiani", 
        "givenName": "Andrea", 
        "id": "sg:person.01036413753.41", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01036413753.41"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Rothamsted Research", 
          "id": "https://www.grid.ac/institutes/grid.418374.d", 
          "name": [
            "Biomathematics and Bioinformatics Dept., Rothamsted Research, Harpenden, United Kingdom"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Rawlings", 
        "givenName": "Chris J.", 
        "id": "sg:person.01136644100.43", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01136644100.43"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Rothamsted Research", 
          "id": "https://www.grid.ac/institutes/grid.418374.d", 
          "name": [
            "Biomathematics and Bioinformatics Dept., Rothamsted Research, Harpenden, United Kingdom"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Kuo", 
        "givenName": "Shao-Chih", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Manchester", 
          "id": "https://www.grid.ac/institutes/grid.5379.8", 
          "name": [
            "School of Computing Science, University of Manchester, Manchester, United Kingdom"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Stevens", 
        "givenName": "Robert", 
        "id": "sg:person.0653547307.62", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0653547307.62"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Newcastle University", 
          "id": "https://www.grid.ac/institutes/grid.1006.7", 
          "name": [
            "School of Compting Science, Newcastle University, Newcastle upon Tyne, United Kingdom"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Lord", 
        "givenName": "Phillip", 
        "id": "sg:person.0776355561.43", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0776355561.43"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1186/1471-2105-9-s4-s6", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004329287", 
          "https://doi.org/10.1186/1471-2105-9-s4-s6"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.4018/jswis.2009081901", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005783792"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btl081", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024625191"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-3-642-13486-9_21", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024958425", 
          "https://doi.org/10.1007/978-3-642-13486-9_21"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-3-642-13486-9_21", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024958425", 
          "https://doi.org/10.1007/978-3-642-13486-9_21"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.jbi.2008.01.008", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042407175"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1756-0381-1-12", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042456290", 
          "https://doi.org/10.1186/1756-0381-1-12"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.1239303", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052744398"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/scientificamerican0501-34", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1056527616", 
          "https://doi.org/10.1038/scientificamerican0501-34"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1089/cmb.1995.2.557", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1059245122"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1089/cmb.1995.2.573", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1059245123"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/stke.2832005pe22", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062692698"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2012", 
    "datePublishedReg": "2012-01-01", 
    "description": "More information is now being published in machine processable form on the web and, as de-facto distributed knowledge bases are materializing, partly encouraged by the vision of the Semantic Web, the focus is shifting from the publication of this information to its consumption. Platforms for data integration, visualization and analysis that are based on a graph representation of information appear first candidates to be consumers of web-based information that is readily expressible as graphs. The question is whether the adoption of these platforms to information available on the Semantic Web requires some adaptation of their data structures and semantics. Ondex is a network-based data integration, analysis and visualization platform which has been developed in a Life Sciences context. A number of features, including semantic annotation via ontologies and an attention to provenance and evidence, make this an ideal candidate to consume Semantic Web information, as well as a prototype for the application of network analysis tools in this context. By analyzing the Ondex data structure and its usage, we have found a set of discrepancies and errors arising from the semantic mismatch between a procedural approach to network analysis and the implications of a web-based representation of information.We report in the paper on the simple methodology that we have adopted to conduct such analysis, and on issues that we have found which may be relevant for a range of similar platforms.", 
    "editor": [
      {
        "familyName": "Gaol", 
        "givenName": "Ford Lumban", 
        "type": "Person"
      }
    ], 
    "genre": "chapter", 
    "id": "sg:pub.10.1007/978-3-642-28798-5_13", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isPartOf": {
      "isbn": [
        "978-3-642-28797-8", 
        "978-3-642-28798-5"
      ], 
      "name": "Recent Progress in Data Engineering and Internet Technology", 
      "type": "Book"
    }, 
    "name": "Lost in Translation: Data Integration Tools Meet the Semantic Web (Experiences from the Ondex Project)", 
    "pagination": "87-97", 
    "productId": [
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/978-3-642-28798-5_13"
        ]
      }, 
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "b55fa078c401931a8fd7150735250b61faedad0233659f56e44af4c83e75ecd9"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1038074257"
        ]
      }
    ], 
    "publisher": {
      "location": "Berlin, Heidelberg", 
      "name": "Springer Berlin Heidelberg", 
      "type": "Organisation"
    }, 
    "sameAs": [
      "https://doi.org/10.1007/978-3-642-28798-5_13", 
      "https://app.dimensions.ai/details/publication/pub.1038074257"
    ], 
    "sdDataset": "chapters", 
    "sdDatePublished": "2019-04-15T18:12", 
    "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_8681_00000266.jsonl", 
    "type": "Chapter", 
    "url": "http://link.springer.com/10.1007/978-3-642-28798-5_13"
  }
]
 

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.10.1007/978-3-642-28798-5_13'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/978-3-642-28798-5_13'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/978-3-642-28798-5_13'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/978-3-642-28798-5_13'


 

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

135 TRIPLES      23 PREDICATES      38 URIs      20 LITERALS      8 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/978-3-642-28798-5_13 schema:about anzsrc-for:08
2 anzsrc-for:0806
3 schema:author N15c73167f78a423fb4647108d11e0e57
4 schema:citation sg:pub.10.1007/978-3-642-13486-9_21
5 sg:pub.10.1038/scientificamerican0501-34
6 sg:pub.10.1186/1471-2105-9-s4-s6
7 sg:pub.10.1186/1756-0381-1-12
8 https://doi.org/10.1016/j.jbi.2008.01.008
9 https://doi.org/10.1089/cmb.1995.2.557
10 https://doi.org/10.1089/cmb.1995.2.573
11 https://doi.org/10.1093/bioinformatics/btl081
12 https://doi.org/10.1101/gr.1239303
13 https://doi.org/10.1126/stke.2832005pe22
14 https://doi.org/10.4018/jswis.2009081901
15 schema:datePublished 2012
16 schema:datePublishedReg 2012-01-01
17 schema:description More information is now being published in machine processable form on the web and, as de-facto distributed knowledge bases are materializing, partly encouraged by the vision of the Semantic Web, the focus is shifting from the publication of this information to its consumption. Platforms for data integration, visualization and analysis that are based on a graph representation of information appear first candidates to be consumers of web-based information that is readily expressible as graphs. The question is whether the adoption of these platforms to information available on the Semantic Web requires some adaptation of their data structures and semantics. Ondex is a network-based data integration, analysis and visualization platform which has been developed in a Life Sciences context. A number of features, including semantic annotation via ontologies and an attention to provenance and evidence, make this an ideal candidate to consume Semantic Web information, as well as a prototype for the application of network analysis tools in this context. By analyzing the Ondex data structure and its usage, we have found a set of discrepancies and errors arising from the semantic mismatch between a procedural approach to network analysis and the implications of a web-based representation of information.We report in the paper on the simple methodology that we have adopted to conduct such analysis, and on issues that we have found which may be relevant for a range of similar platforms.
18 schema:editor N94f3cef7cc564bb7982c466f42e4e729
19 schema:genre chapter
20 schema:inLanguage en
21 schema:isAccessibleForFree true
22 schema:isPartOf Nbdd89ca11b5b475bb714a6c7be5f1657
23 schema:name Lost in Translation: Data Integration Tools Meet the Semantic Web (Experiences from the Ondex Project)
24 schema:pagination 87-97
25 schema:productId N497c55cfef454383bd8b4a968c8f588f
26 N6e208505c2c14cc7ac5bd371b2f53a93
27 Nb6bccf01913140b0aced83699484fb26
28 schema:publisher Ncaae5c4c5a2e471d994a3b61ef9c41ff
29 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038074257
30 https://doi.org/10.1007/978-3-642-28798-5_13
31 schema:sdDatePublished 2019-04-15T18:12
32 schema:sdLicense https://scigraph.springernature.com/explorer/license/
33 schema:sdPublisher N1fc9561a7792454097efd4c5dfb93976
34 schema:url http://link.springer.com/10.1007/978-3-642-28798-5_13
35 sgo:license sg:explorer/license/
36 sgo:sdDataset chapters
37 rdf:type schema:Chapter
38 N15c73167f78a423fb4647108d11e0e57 rdf:first sg:person.01036413753.41
39 rdf:rest Na612da128be148d08cdfbcfb65d450fe
40 N1fc9561a7792454097efd4c5dfb93976 schema:name Springer Nature - SN SciGraph project
41 rdf:type schema:Organization
42 N459d634bd4f74e1bbc8f98d80918e997 schema:affiliation https://www.grid.ac/institutes/grid.418374.d
43 schema:familyName Kuo
44 schema:givenName Shao-Chih
45 rdf:type schema:Person
46 N497c55cfef454383bd8b4a968c8f588f schema:name doi
47 schema:value 10.1007/978-3-642-28798-5_13
48 rdf:type schema:PropertyValue
49 N5c072cb6cd37430cb6e88f575bd04cc4 schema:familyName Gaol
50 schema:givenName Ford Lumban
51 rdf:type schema:Person
52 N67f45ff36fd542dca38cd5b25f93c971 rdf:first sg:person.0653547307.62
53 rdf:rest Na1fd4df13ca54c1b856da66df8de65d1
54 N6e208505c2c14cc7ac5bd371b2f53a93 schema:name readcube_id
55 schema:value b55fa078c401931a8fd7150735250b61faedad0233659f56e44af4c83e75ecd9
56 rdf:type schema:PropertyValue
57 N94f3cef7cc564bb7982c466f42e4e729 rdf:first N5c072cb6cd37430cb6e88f575bd04cc4
58 rdf:rest rdf:nil
59 Na1fd4df13ca54c1b856da66df8de65d1 rdf:first sg:person.0776355561.43
60 rdf:rest rdf:nil
61 Na612da128be148d08cdfbcfb65d450fe rdf:first sg:person.01136644100.43
62 rdf:rest Nc5c121533097476486e7dbab217e6dc0
63 Nb6bccf01913140b0aced83699484fb26 schema:name dimensions_id
64 schema:value pub.1038074257
65 rdf:type schema:PropertyValue
66 Nbdd89ca11b5b475bb714a6c7be5f1657 schema:isbn 978-3-642-28797-8
67 978-3-642-28798-5
68 schema:name Recent Progress in Data Engineering and Internet Technology
69 rdf:type schema:Book
70 Nc5c121533097476486e7dbab217e6dc0 rdf:first N459d634bd4f74e1bbc8f98d80918e997
71 rdf:rest N67f45ff36fd542dca38cd5b25f93c971
72 Ncaae5c4c5a2e471d994a3b61ef9c41ff schema:location Berlin, Heidelberg
73 schema:name Springer Berlin Heidelberg
74 rdf:type schema:Organisation
75 anzsrc-for:08 schema:inDefinedTermSet anzsrc-for:
76 schema:name Information and Computing Sciences
77 rdf:type schema:DefinedTerm
78 anzsrc-for:0806 schema:inDefinedTermSet anzsrc-for:
79 schema:name Information Systems
80 rdf:type schema:DefinedTerm
81 sg:person.01036413753.41 schema:affiliation https://www.grid.ac/institutes/grid.418374.d
82 schema:familyName Splendiani
83 schema:givenName Andrea
84 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01036413753.41
85 rdf:type schema:Person
86 sg:person.01136644100.43 schema:affiliation https://www.grid.ac/institutes/grid.418374.d
87 schema:familyName Rawlings
88 schema:givenName Chris J.
89 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01136644100.43
90 rdf:type schema:Person
91 sg:person.0653547307.62 schema:affiliation https://www.grid.ac/institutes/grid.5379.8
92 schema:familyName Stevens
93 schema:givenName Robert
94 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0653547307.62
95 rdf:type schema:Person
96 sg:person.0776355561.43 schema:affiliation https://www.grid.ac/institutes/grid.1006.7
97 schema:familyName Lord
98 schema:givenName Phillip
99 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0776355561.43
100 rdf:type schema:Person
101 sg:pub.10.1007/978-3-642-13486-9_21 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024958425
102 https://doi.org/10.1007/978-3-642-13486-9_21
103 rdf:type schema:CreativeWork
104 sg:pub.10.1038/scientificamerican0501-34 schema:sameAs https://app.dimensions.ai/details/publication/pub.1056527616
105 https://doi.org/10.1038/scientificamerican0501-34
106 rdf:type schema:CreativeWork
107 sg:pub.10.1186/1471-2105-9-s4-s6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004329287
108 https://doi.org/10.1186/1471-2105-9-s4-s6
109 rdf:type schema:CreativeWork
110 sg:pub.10.1186/1756-0381-1-12 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042456290
111 https://doi.org/10.1186/1756-0381-1-12
112 rdf:type schema:CreativeWork
113 https://doi.org/10.1016/j.jbi.2008.01.008 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042407175
114 rdf:type schema:CreativeWork
115 https://doi.org/10.1089/cmb.1995.2.557 schema:sameAs https://app.dimensions.ai/details/publication/pub.1059245122
116 rdf:type schema:CreativeWork
117 https://doi.org/10.1089/cmb.1995.2.573 schema:sameAs https://app.dimensions.ai/details/publication/pub.1059245123
118 rdf:type schema:CreativeWork
119 https://doi.org/10.1093/bioinformatics/btl081 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024625191
120 rdf:type schema:CreativeWork
121 https://doi.org/10.1101/gr.1239303 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052744398
122 rdf:type schema:CreativeWork
123 https://doi.org/10.1126/stke.2832005pe22 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062692698
124 rdf:type schema:CreativeWork
125 https://doi.org/10.4018/jswis.2009081901 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005783792
126 rdf:type schema:CreativeWork
127 https://www.grid.ac/institutes/grid.1006.7 schema:alternateName Newcastle University
128 schema:name School of Compting Science, Newcastle University, Newcastle upon Tyne, United Kingdom
129 rdf:type schema:Organization
130 https://www.grid.ac/institutes/grid.418374.d schema:alternateName Rothamsted Research
131 schema:name Biomathematics and Bioinformatics Dept., Rothamsted Research, Harpenden, United Kingdom
132 rdf:type schema:Organization
133 https://www.grid.ac/institutes/grid.5379.8 schema:alternateName University of Manchester
134 schema:name School of Computing Science, University of Manchester, Manchester, United Kingdom
135 rdf:type schema:Organization
 




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


...