Distributed Processing of Large BioMedical 3D Images View Full Text


Ontology type: schema:Chapter      Open Access: True


Chapter Info

DATE

2005

AUTHORS

Konstantinos Liakos , Albert Burger , Richard Baldock

ABSTRACT

The Human Genetics Unit (HGU) of the Medical Research Council (MRC) in Edinburgh has developed the Edinburgh Mouse Atlas, a spatial temporal framework to store and analyze biological data including 3D images that relate to mouse embryo development. The purpose of the system is the analysis and querying of complex spatial patterns in particular the patterns of gene activity during embryo development. The framework holds large 3D grey level images and is implemented in part as an object-oriented database. In this paper we propose a layered architecture, based on the mediator approach, for the design of a transparent, and scalable distributed system which can process objects that can exceed 1GB in size. The system’s data are distributed and/or declustered, across a number of image servers and are processed by specialized mediators. More... »

PAGES

142-155

References to SciGraph publications

Book

TITLE

High Performance Computing for Computational Science - VECPAR 2004

ISBN

978-3-540-25424-9
978-3-540-31854-5

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/11403937_12

DOI

http://dx.doi.org/10.1007/11403937_12

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1030872128


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": "Medical Research Council Institute of Genetics and Molecular Medicine", 
          "id": "https://www.grid.ac/institutes/grid.415854.9", 
          "name": [
            "School of Mathematical and Computer Sciences, Heriot-Watt University, Ricarton Campus, EH14 4S, Edinburgh, Scotland, UK", 
            "MRC Human Genetics Unit, Western Hospital, Crewe Road, EH4 2XU, Edinburgh, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Liakos", 
        "givenName": "Konstantinos", 
        "id": "sg:person.01127312304.55", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01127312304.55"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Medical Research Council Institute of Genetics and Molecular Medicine", 
          "id": "https://www.grid.ac/institutes/grid.415854.9", 
          "name": [
            "School of Mathematical and Computer Sciences, Heriot-Watt University, Ricarton Campus, EH14 4S, Edinburgh, Scotland, UK", 
            "MRC Human Genetics Unit, Western Hospital, Crewe Road, EH4 2XU, Edinburgh, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Burger", 
        "givenName": "Albert", 
        "id": "sg:person.0722741153.95", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0722741153.95"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Medical Research Council Institute of Genetics and Molecular Medicine", 
          "id": "https://www.grid.ac/institutes/grid.415854.9", 
          "name": [
            "MRC Human Genetics Unit, Western Hospital, Crewe Road, EH4 2XU, Edinburgh, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Baldock", 
        "givenName": "Richard", 
        "id": "sg:person.0623503461.12", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0623503461.12"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1007/978-3-642-88418-4", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017519325", 
          "https://doi.org/10.1007/978-3-642-88418-4"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-3-642-88418-4", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017519325", 
          "https://doi.org/10.1007/978-3-642-88418-4"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1006/scdb.1997.0175", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018450807"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/14.2.112", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024497656"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1145/288627.288662", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037846360"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/bies.950140713", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039126294"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/cpe.607", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1048174919"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1109/2.121508", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1061105048"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1109/69.729736", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1061213706"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.8091224", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062652229"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1109/coopis.1999.792178", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1093182953"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1109/ssdm.2001.938553", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1093812261"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1109/icde.1994.283037", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1093884647"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1109/iciis.1999.810219", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1095139631"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1109/adl.2000.848396", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1095299232"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1201/9781420036206", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1095905324"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2005", 
    "datePublishedReg": "2005-01-01", 
    "description": "The Human Genetics Unit (HGU) of the Medical Research Council (MRC) in Edinburgh has developed the Edinburgh Mouse Atlas, a spatial temporal framework to store and analyze biological data including 3D images that relate to mouse embryo development. The purpose of the system is the analysis and querying of complex spatial patterns in particular the patterns of gene activity during embryo development. The framework holds large 3D grey level images and is implemented in part as an object-oriented database. In this paper we propose a layered architecture, based on the mediator approach, for the design of a transparent, and scalable distributed system which can process objects that can exceed 1GB in size. The system\u2019s data are distributed and/or declustered, across a number of image servers and are processed by specialized mediators.", 
    "editor": [
      {
        "familyName": "Dayd\u00e9", 
        "givenName": "Michel", 
        "type": "Person"
      }, 
      {
        "familyName": "Dongarra", 
        "givenName": "Jack", 
        "type": "Person"
      }, 
      {
        "familyName": "Hern\u00e1ndez", 
        "givenName": "Vicente", 
        "type": "Person"
      }, 
      {
        "familyName": "Palma", 
        "givenName": "Jos\u00e9 M. L. M.", 
        "type": "Person"
      }
    ], 
    "genre": "chapter", 
    "id": "sg:pub.10.1007/11403937_12", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isPartOf": {
      "isbn": [
        "978-3-540-25424-9", 
        "978-3-540-31854-5"
      ], 
      "name": "High Performance Computing for Computational Science - VECPAR 2004", 
      "type": "Book"
    }, 
    "name": "Distributed Processing of Large BioMedical 3D Images", 
    "pagination": "142-155", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1030872128"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/11403937_12"
        ]
      }, 
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "9312158231531d5c8a67601335b148f09912c5a58412ad9668bc3d3e333bdf67"
        ]
      }
    ], 
    "publisher": {
      "location": "Berlin, Heidelberg", 
      "name": "Springer Berlin Heidelberg", 
      "type": "Organisation"
    }, 
    "sameAs": [
      "https://doi.org/10.1007/11403937_12", 
      "https://app.dimensions.ai/details/publication/pub.1030872128"
    ], 
    "sdDataset": "chapters", 
    "sdDatePublished": "2019-04-16T08:03", 
    "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/v90/0000000359_0000000359/records_29207_00000001.jsonl", 
    "type": "Chapter", 
    "url": "https://link.springer.com/10.1007%2F11403937_12"
  }
]
 

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.10.1007/11403937_12'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/11403937_12'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/11403937_12'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/11403937_12'


 

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

141 TRIPLES      23 PREDICATES      42 URIs      20 LITERALS      8 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/11403937_12 schema:about anzsrc-for:08
2 anzsrc-for:0806
3 schema:author N25a094365b9b4cfbb12e2fff839c5b18
4 schema:citation sg:pub.10.1007/978-3-642-88418-4
5 https://doi.org/10.1002/bies.950140713
6 https://doi.org/10.1002/cpe.607
7 https://doi.org/10.1006/scdb.1997.0175
8 https://doi.org/10.1093/bioinformatics/14.2.112
9 https://doi.org/10.1109/2.121508
10 https://doi.org/10.1109/69.729736
11 https://doi.org/10.1109/adl.2000.848396
12 https://doi.org/10.1109/coopis.1999.792178
13 https://doi.org/10.1109/icde.1994.283037
14 https://doi.org/10.1109/iciis.1999.810219
15 https://doi.org/10.1109/ssdm.2001.938553
16 https://doi.org/10.1126/science.8091224
17 https://doi.org/10.1145/288627.288662
18 https://doi.org/10.1201/9781420036206
19 schema:datePublished 2005
20 schema:datePublishedReg 2005-01-01
21 schema:description The Human Genetics Unit (HGU) of the Medical Research Council (MRC) in Edinburgh has developed the Edinburgh Mouse Atlas, a spatial temporal framework to store and analyze biological data including 3D images that relate to mouse embryo development. The purpose of the system is the analysis and querying of complex spatial patterns in particular the patterns of gene activity during embryo development. The framework holds large 3D grey level images and is implemented in part as an object-oriented database. In this paper we propose a layered architecture, based on the mediator approach, for the design of a transparent, and scalable distributed system which can process objects that can exceed 1GB in size. The system’s data are distributed and/or declustered, across a number of image servers and are processed by specialized mediators.
22 schema:editor N7ea33277be0a48f9ac1c0cde259c5637
23 schema:genre chapter
24 schema:inLanguage en
25 schema:isAccessibleForFree true
26 schema:isPartOf N1d50ccee04dd47f3894a3b223659a110
27 schema:name Distributed Processing of Large BioMedical 3D Images
28 schema:pagination 142-155
29 schema:productId N693e11c61a4a4becb273fcf6524163a8
30 N905e75f2a4af40ea9fec3f24b2642094
31 Nce2b5bcee4514510b620e2838cc7de78
32 schema:publisher N0166fc11fbdc4c3980b8da4b837d8d03
33 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030872128
34 https://doi.org/10.1007/11403937_12
35 schema:sdDatePublished 2019-04-16T08:03
36 schema:sdLicense https://scigraph.springernature.com/explorer/license/
37 schema:sdPublisher N85bd7f09d0194641b0413de3a8b1884b
38 schema:url https://link.springer.com/10.1007%2F11403937_12
39 sgo:license sg:explorer/license/
40 sgo:sdDataset chapters
41 rdf:type schema:Chapter
42 N0166fc11fbdc4c3980b8da4b837d8d03 schema:location Berlin, Heidelberg
43 schema:name Springer Berlin Heidelberg
44 rdf:type schema:Organisation
45 N048c1f69fe2d408090df1c4ba22d79d9 rdf:first N1f299756929e4348ada62ac4945290df
46 rdf:rest Ncbc5ccab6f6e420bbb6ef4ab8f05a982
47 N1d50ccee04dd47f3894a3b223659a110 schema:isbn 978-3-540-25424-9
48 978-3-540-31854-5
49 schema:name High Performance Computing for Computational Science - VECPAR 2004
50 rdf:type schema:Book
51 N1f299756929e4348ada62ac4945290df schema:familyName Dongarra
52 schema:givenName Jack
53 rdf:type schema:Person
54 N20dda2af6e68436bb0b352d30eaf5aed rdf:first N362c04c190544621bf95de3991315bac
55 rdf:rest rdf:nil
56 N25a094365b9b4cfbb12e2fff839c5b18 rdf:first sg:person.01127312304.55
57 rdf:rest Nc44a5e644de64eec9a7b64dab9d2e270
58 N33be35247d7f4e4894a60a9927d2f102 rdf:first sg:person.0623503461.12
59 rdf:rest rdf:nil
60 N362c04c190544621bf95de3991315bac schema:familyName Palma
61 schema:givenName José M. L. M.
62 rdf:type schema:Person
63 N54e109f3c267499bb6b2d0df1b900934 schema:familyName Daydé
64 schema:givenName Michel
65 rdf:type schema:Person
66 N693e11c61a4a4becb273fcf6524163a8 schema:name readcube_id
67 schema:value 9312158231531d5c8a67601335b148f09912c5a58412ad9668bc3d3e333bdf67
68 rdf:type schema:PropertyValue
69 N7ea33277be0a48f9ac1c0cde259c5637 rdf:first N54e109f3c267499bb6b2d0df1b900934
70 rdf:rest N048c1f69fe2d408090df1c4ba22d79d9
71 N85bd7f09d0194641b0413de3a8b1884b schema:name Springer Nature - SN SciGraph project
72 rdf:type schema:Organization
73 N905e75f2a4af40ea9fec3f24b2642094 schema:name doi
74 schema:value 10.1007/11403937_12
75 rdf:type schema:PropertyValue
76 Nacac458f3b6c4f9cb05270251a892918 schema:familyName Hernández
77 schema:givenName Vicente
78 rdf:type schema:Person
79 Nc44a5e644de64eec9a7b64dab9d2e270 rdf:first sg:person.0722741153.95
80 rdf:rest N33be35247d7f4e4894a60a9927d2f102
81 Ncbc5ccab6f6e420bbb6ef4ab8f05a982 rdf:first Nacac458f3b6c4f9cb05270251a892918
82 rdf:rest N20dda2af6e68436bb0b352d30eaf5aed
83 Nce2b5bcee4514510b620e2838cc7de78 schema:name dimensions_id
84 schema:value pub.1030872128
85 rdf:type schema:PropertyValue
86 anzsrc-for:08 schema:inDefinedTermSet anzsrc-for:
87 schema:name Information and Computing Sciences
88 rdf:type schema:DefinedTerm
89 anzsrc-for:0806 schema:inDefinedTermSet anzsrc-for:
90 schema:name Information Systems
91 rdf:type schema:DefinedTerm
92 sg:person.01127312304.55 schema:affiliation https://www.grid.ac/institutes/grid.415854.9
93 schema:familyName Liakos
94 schema:givenName Konstantinos
95 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01127312304.55
96 rdf:type schema:Person
97 sg:person.0623503461.12 schema:affiliation https://www.grid.ac/institutes/grid.415854.9
98 schema:familyName Baldock
99 schema:givenName Richard
100 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0623503461.12
101 rdf:type schema:Person
102 sg:person.0722741153.95 schema:affiliation https://www.grid.ac/institutes/grid.415854.9
103 schema:familyName Burger
104 schema:givenName Albert
105 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0722741153.95
106 rdf:type schema:Person
107 sg:pub.10.1007/978-3-642-88418-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017519325
108 https://doi.org/10.1007/978-3-642-88418-4
109 rdf:type schema:CreativeWork
110 https://doi.org/10.1002/bies.950140713 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039126294
111 rdf:type schema:CreativeWork
112 https://doi.org/10.1002/cpe.607 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048174919
113 rdf:type schema:CreativeWork
114 https://doi.org/10.1006/scdb.1997.0175 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018450807
115 rdf:type schema:CreativeWork
116 https://doi.org/10.1093/bioinformatics/14.2.112 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024497656
117 rdf:type schema:CreativeWork
118 https://doi.org/10.1109/2.121508 schema:sameAs https://app.dimensions.ai/details/publication/pub.1061105048
119 rdf:type schema:CreativeWork
120 https://doi.org/10.1109/69.729736 schema:sameAs https://app.dimensions.ai/details/publication/pub.1061213706
121 rdf:type schema:CreativeWork
122 https://doi.org/10.1109/adl.2000.848396 schema:sameAs https://app.dimensions.ai/details/publication/pub.1095299232
123 rdf:type schema:CreativeWork
124 https://doi.org/10.1109/coopis.1999.792178 schema:sameAs https://app.dimensions.ai/details/publication/pub.1093182953
125 rdf:type schema:CreativeWork
126 https://doi.org/10.1109/icde.1994.283037 schema:sameAs https://app.dimensions.ai/details/publication/pub.1093884647
127 rdf:type schema:CreativeWork
128 https://doi.org/10.1109/iciis.1999.810219 schema:sameAs https://app.dimensions.ai/details/publication/pub.1095139631
129 rdf:type schema:CreativeWork
130 https://doi.org/10.1109/ssdm.2001.938553 schema:sameAs https://app.dimensions.ai/details/publication/pub.1093812261
131 rdf:type schema:CreativeWork
132 https://doi.org/10.1126/science.8091224 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062652229
133 rdf:type schema:CreativeWork
134 https://doi.org/10.1145/288627.288662 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037846360
135 rdf:type schema:CreativeWork
136 https://doi.org/10.1201/9781420036206 schema:sameAs https://app.dimensions.ai/details/publication/pub.1095905324
137 rdf:type schema:CreativeWork
138 https://www.grid.ac/institutes/grid.415854.9 schema:alternateName Medical Research Council Institute of Genetics and Molecular Medicine
139 schema:name MRC Human Genetics Unit, Western Hospital, Crewe Road, EH4 2XU, Edinburgh, UK
140 School of Mathematical and Computer Sciences, Heriot-Watt University, Ricarton Campus, EH14 4S, Edinburgh, Scotland, UK
141 rdf:type schema:Organization
 




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


...