rof 1.0.7 → 1.2.0

Sign up to get free protection for your applications and to get access to all the features.
Files changed (90) hide show
  1. checksums.yaml +4 -4
  2. data/.travis.yml +9 -7
  3. data/LICENSE +201 -16
  4. data/Rakefile +46 -0
  5. data/bin/csv_to_rof +1 -2
  6. data/bin/fedora_to_rof +7 -1
  7. data/bin/jsonld_to_rof +26 -0
  8. data/bin/osf_to_rof +6 -2
  9. data/bin/rof +5 -19
  10. data/lib/rof.rb +2 -6
  11. data/lib/rof/access.rb +1 -1
  12. data/lib/rof/cli.rb +104 -67
  13. data/lib/rof/compare_rof.rb +68 -39
  14. data/lib/rof/filter.rb +21 -0
  15. data/lib/rof/filters.rb +38 -0
  16. data/lib/rof/filters/bendo.rb +15 -17
  17. data/lib/rof/filters/date_stamp.rb +5 -4
  18. data/lib/rof/filters/file_to_url.rb +5 -3
  19. data/lib/rof/filters/label.rb +9 -7
  20. data/lib/rof/filters/work.rb +7 -5
  21. data/lib/rof/ingest.rb +5 -0
  22. data/lib/rof/osf_context.rb +2 -2
  23. data/lib/rof/rdf_context.rb +2 -0
  24. data/lib/rof/translator.rb +18 -0
  25. data/lib/rof/translators.rb +23 -0
  26. data/lib/rof/{translate_csv.rb → translators/csv_to_rof.rb} +4 -3
  27. data/lib/rof/translators/fedora_to_rof.rb +244 -0
  28. data/lib/rof/translators/jsonld_to_rof.rb +112 -0
  29. data/lib/rof/translators/jsonld_to_rof/accumulator.rb +175 -0
  30. data/lib/rof/translators/jsonld_to_rof/predicate_handler.rb +223 -0
  31. data/lib/rof/translators/jsonld_to_rof/predicate_object_handler.rb +125 -0
  32. data/lib/rof/translators/jsonld_to_rof/statement_handler.rb +91 -0
  33. data/lib/rof/translators/osf_to_rof.rb +191 -0
  34. data/lib/rof/utility.rb +44 -1
  35. data/lib/rof/version.rb +1 -1
  36. data/rof.gemspec +10 -2
  37. data/spec/coverage_helper.rb +17 -0
  38. data/spec/fixtures/for_utility_load_items_from_json_file/multiple_items.json +8 -0
  39. data/spec/fixtures/for_utility_load_items_from_json_file/parse_error.json +3 -0
  40. data/spec/fixtures/for_utility_load_items_from_json_file/single_item.json +3 -0
  41. data/spec/fixtures/jsonld_to_rof/0g354f18610.jsonld +113 -0
  42. data/spec/fixtures/jsonld_to_rof/0g354f18610.rof +96 -0
  43. data/spec/fixtures/jsonld_to_rof/2j62s467216.jsonld +113 -0
  44. data/spec/fixtures/jsonld_to_rof/2j62s467216.rof +93 -0
  45. data/spec/fixtures/jsonld_to_rof/2v23vt16z2z.jsonld +70 -0
  46. data/spec/fixtures/jsonld_to_rof/2v23vt16z2z.rof +87 -0
  47. data/spec/fixtures/jsonld_to_rof/cr56n01253w.jsonld +84 -0
  48. data/spec/fixtures/jsonld_to_rof/cr56n01253w.rof +95 -0
  49. data/spec/fixtures/jsonld_to_rof/h989r21069m.jsonld +84 -0
  50. data/spec/fixtures/jsonld_to_rof/h989r21069m.rof +98 -0
  51. data/spec/fixtures/jsonld_to_rof/js956d59913.jsonld +79 -0
  52. data/spec/fixtures/jsonld_to_rof/js956d59913.rof +89 -0
  53. data/spec/fixtures/jsonld_to_rof/m039k358q5c.jsonld +80 -0
  54. data/spec/fixtures/jsonld_to_rof/m039k358q5c.rof +64 -0
  55. data/spec/fixtures/jsonld_to_rof/nk322b9161g.jsonld +89 -0
  56. data/spec/fixtures/jsonld_to_rof/nk322b9161g.rof +69 -0
  57. data/spec/fixtures/jsonld_to_rof/p8418k7430d.jsonld +84 -0
  58. data/spec/fixtures/jsonld_to_rof/p8418k7430d.rof +67 -0
  59. data/spec/fixtures/jsonld_to_rof/xg94hm53h0c.jsonld +98 -0
  60. data/spec/fixtures/jsonld_to_rof/xg94hm53h0c.rof +110 -0
  61. data/spec/fixtures/jsonld_to_rof/zk51vd69n1r.jsonld +94 -0
  62. data/spec/fixtures/jsonld_to_rof/zk51vd69n1r.rof +121 -0
  63. data/spec/fixtures/osf/phz6b.tar.gz +0 -0
  64. data/spec/lib/rof/access_spec.rb +30 -23
  65. data/spec/lib/rof/cli_spec.rb +83 -60
  66. data/spec/lib/rof/compare_rof_spec.rb +35 -24
  67. data/spec/lib/rof/filter_spec.rb +10 -0
  68. data/spec/lib/rof/filters/bendo_spec.rb +42 -0
  69. data/spec/lib/rof/filters/date_stamp_spec.rb +9 -5
  70. data/spec/lib/rof/filters/file_to_url_spec.rb +7 -3
  71. data/spec/lib/rof/filters/label_spec.rb +121 -77
  72. data/spec/lib/rof/filters/work_spec.rb +7 -4
  73. data/spec/lib/rof/filters_spec.rb +14 -0
  74. data/spec/lib/rof/translator_spec.rb +15 -0
  75. data/spec/lib/rof/{translate_csv_spec.rb → translators/csv_to_rof_spec.rb} +14 -14
  76. data/spec/lib/rof/translators/fedora_to_rof_spec.rb +64 -0
  77. data/spec/lib/rof/translators/jsonld_to_rof/accumulator_spec.rb +121 -0
  78. data/spec/lib/rof/translators/jsonld_to_rof/predicate_handler_spec.rb +73 -0
  79. data/spec/lib/rof/translators/jsonld_to_rof/predicate_object_handler_spec.rb +48 -0
  80. data/spec/lib/rof/translators/jsonld_to_rof/statement_handler_spec.rb +40 -0
  81. data/spec/lib/rof/translators/jsonld_to_rof_spec.rb +120 -0
  82. data/spec/lib/rof/{osf_to_rof_spec.rb → translators/osf_to_rof_spec.rb} +55 -25
  83. data/spec/lib/rof/translators_spec.rb +14 -0
  84. data/spec/lib/rof/utility_spec.rb +47 -1
  85. data/spec/spec_helper.rb +1 -1
  86. data/spec/support/an_rof_filter.rb +10 -0
  87. metadata +186 -15
  88. data/lib/rof/get_from_fedora.rb +0 -211
  89. data/lib/rof/osf_to_rof.rb +0 -123
  90. data/spec/lib/rof/get_from_fedora_spec.rb +0 -22
@@ -0,0 +1,69 @@
1
+ [
2
+ {
3
+ "type": "fobject",
4
+ "af-model": "Document",
5
+ "pid": "und:nk322b9161g",
6
+ "bendo-item": "j6731259p70",
7
+ "rights": {
8
+ "read-groups": [
9
+ "public"
10
+ ],
11
+ "edit": [
12
+ "rtillman,vpattiso"
13
+ ]
14
+ },
15
+ "properties": "<fields><depositor>batch_ingest</depositor>\n<owner>rtillman,vpattiso</owner>\n<representative>und:np193774g25</representative>\n</fields>\n",
16
+ "properties-meta": {
17
+ "mime-type": "text/xml"
18
+ },
19
+ "rels-ext": {
20
+ "isMemberOfCollection": [
21
+ "und:j098z893451"
22
+ ]
23
+ },
24
+ "metadata": {
25
+ "dc:type": "Report",
26
+ "dc:title": "Equipped To Serve: Latino/a Seminarians and the Future of Religious Leadership in the Latino/a Community",
27
+ "dc:creator": [
28
+ "Milagros Pe\\u00F1a",
29
+ "Edwin I. Hern\\u00E1ndez",
30
+ "Caroline Sotelo-Turner",
31
+ "Danielle Dirks",
32
+ "Kari Jo Verhulst"
33
+ ],
34
+ "dc:abstract": "Describes the next generation of Latino/a religious leaders and examines the effectiveness of their theological education. Identifies critical institutional and curricular characteristics for preparing seminarians to be leaders responding to spiritual and material needs of Latinos/as in U.S. Based upon data from focus groups and surveys conducted in 2002-2004.",
35
+ "dc:subject": [
36
+ "Education",
37
+ "Religion"
38
+ ],
39
+ "dc:created": "2006-10-01",
40
+ "dc:creator#administrative_unit": "University of Notre Dame::Centers and Institutes::Institute for Latino Studies",
41
+ "dc:rights": "All rights reserved",
42
+ "dc:language": "English",
43
+ "@context": {
44
+ "bibo": "http://purl.org/ontology/bibo/",
45
+ "dc": "http://purl.org/dc/terms/",
46
+ "ebucore": "http://www.ebu.ch/metadata/ontologies/ebucore/ebucore#",
47
+ "foaf": "http://xmlns.com/foaf/0.1/",
48
+ "hydramata-rel": "http://projecthydra.org/ns/relations#",
49
+ "mrel": "http://id.loc.gov/vocabulary/relators/",
50
+ "ms": "http://www.ndltd.org/standards/metadata/etdms/1.1/",
51
+ "nd": "https://library.nd.edu/ns/terms/",
52
+ "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
53
+ "ths": "http://id.loc.gov/vocabulary/relators/",
54
+ "vracore": "http://purl.org/vra/",
55
+ "dc:dateSubmitted": {
56
+ "@type": "http://www.w3.org/2001/XMLSchema#date"
57
+ },
58
+ "dc:created": {
59
+ "@type": "http://www.w3.org/2001/XMLSchema#date"
60
+ },
61
+ "dc:modified": {
62
+ "@type": "http://www.w3.org/2001/XMLSchema#date"
63
+ }
64
+ },
65
+ "dc:dateSubmitted": "2016-12-15Z",
66
+ "dc:modified": "2016-12-15Z"
67
+ }
68
+ }
69
+ ]
@@ -0,0 +1,84 @@
1
+ {
2
+ "@context": {
3
+ "und": "https://curate.nd.edu/show/",
4
+ "bibo": "http://purl.org/ontology/bibo/",
5
+ "dc": "http://purl.org/dc/terms/",
6
+ "ebucore": "http://www.ebu.ch/metadata/ontologies/ebucore/ebucore#",
7
+ "foaf": "http://xmlns.com/foaf/0.1/",
8
+ "mrel": "http://id.loc.gov/vocabulary/relators/",
9
+ "nd": "https://library.nd.edu/ns/terms/",
10
+ "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
11
+ "vracore": "http://purl.org/vra/",
12
+ "frels": "info:fedora/fedora-system:def/relations-external#",
13
+ "ms": "http://www.ndltd.org/standards/metadata/etdms/1.1/",
14
+ "pav": "http://purl.org/pav/",
15
+ "fedora-model": "info:fedora/fedora-system:def/model#",
16
+ "hydra": "http://projecthydra.org/ns/relations#",
17
+ "hasModel": {
18
+ "@id": "fedora-model:hasModel",
19
+ "@type": "@id"
20
+ },
21
+ "hasEditor": {
22
+ "@id": "hydra:hasEditor",
23
+ "@type": "@id"
24
+ },
25
+ "hasEditorGroup": {
26
+ "@id": "hydra:hasEditorGroup",
27
+ "@type": "@id"
28
+ },
29
+ "isPartOf": {
30
+ "@id": "frels:isPartOf",
31
+ "@type": "@id"
32
+ },
33
+ "isMemberOfCollection": {
34
+ "@id": "frels:isMemberOfCollection",
35
+ "@type": "@id"
36
+ },
37
+ "isEditorOf": {
38
+ "@id": "hydra:isEditorOf",
39
+ "@type": "@id"
40
+ },
41
+ "hasMember": {
42
+ "@id": "frels:hasMember",
43
+ "@type": "@id"
44
+ },
45
+ "previousVersion": "pav:previousVersion"
46
+ },
47
+ "@id": "und:p8418k7430d",
48
+ "dc:creator": ["Kai Zeng", "Charles Addison Bouman Jr.", "Bruno Kristiaan Bernard De Man", "Jiang Hsieh", "Ken David Sauer", "Jean-Baptiste Daniel Marie Thibault", "Zhou Yu"],
49
+ "dc:creator#administrative_unit": "University of Notre Dame::College of Engineering::Electrical Engineering",
50
+ "dc:creator#local": "Ken David Sauer",
51
+ "dc:date#application": "2009-10-28",
52
+ "dc:date#prior_publication": "2011-04-28",
53
+ "dc:dateSubmitted": {
54
+ "@value": "2016-06-07Z",
55
+ "@type": "http://www.w3.org/2001/XMLSchema#date"
56
+ },
57
+ "dc:description": "An improved iterative reconstruction method to reconstruct a first image includes generating an imaging beam, receiving said imaging beam on a detector array, generating projection data based on said imaging beams received by said detector array, providing said projection data to an image reconstructor, enlarging one of a plurality of voxels and a plurality of detectors of the provided projection data, reconstructing portions of the first image with the plurality of enlarged voxels or detectors, and iteratively reconstructing the portions of the first image to create a reconstructed image.",
58
+ "dc:extent#claims": "32",
59
+ "dc:identifier#other_application": "12/607,309",
60
+ "dc:identifier#patent": "US 8655033 B2",
61
+ "dc:identifier#prior_publication": "US 20110097007 A1",
62
+ "dc:issued": "2014-02-18",
63
+ "dc:language": "eng",
64
+ "dc:modified": {
65
+ "@value": "2016-06-07Z",
66
+ "@type": "http://www.w3.org/2001/XMLSchema#date"
67
+ },
68
+ "dc:publisher": "United States Patent and Trademark Office",
69
+ "dc:rights": "http://creativecommons.org/publicdomain/zero/1.0/",
70
+ "dc:rightsHolder": ["University of Notre Dame Du Lac", "General Electric Company (Schenectady, NY)", "Purdue Research Foundation (West Lafayette, IN)"],
71
+ "dc:source": "http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/8655033",
72
+ "dc:subject#cpc": "G06T 11/006 (20130101); G06T 2211/424 (20130101)",
73
+ "dc:subject#ipc": "G06K 9/00",
74
+ "dc:subject#uspc": "382/128; 382/131;",
75
+ "dc:title": "Iterative Reconstruction",
76
+ "nd:accessEdit": "rtillman",
77
+ "nd:accessReadGroup": "public",
78
+ "nd:afmodel": "Patent",
79
+ "nd:depositor": "batch_ingest",
80
+ "nd:owner": "rtillman",
81
+ "nd:representativeFile": {
82
+ "@id": "und:pc289g57c13"
83
+ }
84
+ }
@@ -0,0 +1,67 @@
1
+ [
2
+ {
3
+ "type": "fobject",
4
+ "af-model": "Patent",
5
+ "pid": "und:p8418k7430d",
6
+ "rights": {
7
+ "read-groups": [
8
+ "public"
9
+ ],
10
+ "edit": [
11
+ "rtillman"
12
+ ]
13
+ },
14
+ "properties": "<fields>\n<depositor>batch_ingest</depositor>\n<owner>rtillman</owner>\n<representative>und:pc289g57c13</representative>\n</fields>\n",
15
+ "properties-meta": {
16
+ "mime-type": "text/xml"
17
+ },
18
+ "collections": null,
19
+ "metadata": {
20
+ "dc:identifier#patent": "US 8655033 B2",
21
+ "dc:creator#administrative_unit": "University of Notre Dame::College of Engineering::Electrical Engineering",
22
+ "dc:source": "http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/8655033",
23
+ "dc:issued": "2014-02-18",
24
+ "dc:title": "Iterative Reconstruction",
25
+ "dc:description": "An improved iterative reconstruction method to reconstruct a first image includes generating an imaging beam, receiving said imaging beam on a detector array, generating projection data based on said imaging beams received by said detector array, providing said projection data to an image reconstructor, enlarging one of a plurality of voxels and a plurality of detectors of the provided projection data, reconstructing portions of the first image with the plurality of enlarged voxels or detectors, and iteratively reconstructing the portions of the first image to create a reconstructed image.",
26
+ "dc:creator": [
27
+ "Kai Zeng",
28
+ "Charles Addison Bouman Jr.",
29
+ "Bruno Kristiaan Bernard De Man",
30
+ "Jiang Hsieh",
31
+ "Ken David Sauer",
32
+ "Jean-Baptiste Daniel Marie Thibault",
33
+ "Zhou Yu"
34
+ ],
35
+ "dc:rightsHolder": [
36
+ "University of Notre Dame Du Lac",
37
+ "General Electric Company (Schenectady, NY)",
38
+ "Purdue Research Foundation (West Lafayette, IN)"
39
+ ],
40
+ "dc:identifier#other_application": "12/607,309",
41
+ "dc:date#application": "2009-10-28",
42
+ "dc:date#prior_publication": "2011-04-28",
43
+ "dc:identifier#prior_publication": "US 20110097007 A1",
44
+ "dc:extent#claims": "32",
45
+ "dc:subject#uspc": "382/128; 382/131;",
46
+ "dc:subject#cpc": "G06T 11/006 (20130101); G06T 2211/424 (20130101)",
47
+ "dc:subject#ipc": "G06K 9/00",
48
+ "dc:creator#local": "Ken David Sauer",
49
+ "dc:publisher": "United States Patent and Trademark Office",
50
+ "dc:language": "eng",
51
+ "dc:rights": "http://creativecommons.org/publicdomain/zero/1.0/",
52
+ "@context": {
53
+ "dc": "http://purl.org/dc/terms/",
54
+ "foaf": "http://xmlns.com/foaf/0.1/",
55
+ "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
56
+ "dc:dateSubmitted": {
57
+ "@type": "http://www.w3.org/2001/XMLSchema#date"
58
+ },
59
+ "dc:modified": {
60
+ "@type": "http://www.w3.org/2001/XMLSchema#date"
61
+ }
62
+ },
63
+ "dc:dateSubmitted": "2016-06-07Z",
64
+ "dc:modified": "2016-06-07Z"
65
+ }
66
+ }
67
+ ]
@@ -0,0 +1,98 @@
1
+ {
2
+ "@context": {
3
+ "und": "https://curate.nd.edu/show/",
4
+ "bibo": "http://purl.org/ontology/bibo/",
5
+ "dc": "http://purl.org/dc/terms/",
6
+ "ebucore": "http://www.ebu.ch/metadata/ontologies/ebucore/ebucore#",
7
+ "foaf": "http://xmlns.com/foaf/0.1/",
8
+ "mrel": "http://id.loc.gov/vocabulary/relators/",
9
+ "nd": "https://library.nd.edu/ns/terms/",
10
+ "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
11
+ "vracore": "http://purl.org/vra/",
12
+ "frels": "info:fedora/fedora-system:def/relations-external#",
13
+ "ms": "http://www.ndltd.org/standards/metadata/etdms/1.1/",
14
+ "pav": "http://purl.org/pav/",
15
+ "fedora-model": "info:fedora/fedora-system:def/model#",
16
+ "hydra": "http://projecthydra.org/ns/relations#",
17
+ "hasModel": {
18
+ "@id": "fedora-model:hasModel",
19
+ "@type": "@id"
20
+ },
21
+ "hasEditor": {
22
+ "@id": "hydra:hasEditor",
23
+ "@type": "@id"
24
+ },
25
+ "hasEditorGroup": {
26
+ "@id": "hydra:hasEditorGroup",
27
+ "@type": "@id"
28
+ },
29
+ "isPartOf": {
30
+ "@id": "frels:isPartOf",
31
+ "@type": "@id"
32
+ },
33
+ "isMemberOfCollection": {
34
+ "@id": "frels:isMemberOfCollection",
35
+ "@type": "@id"
36
+ },
37
+ "isEditorOf": {
38
+ "@id": "hydra:isEditorOf",
39
+ "@type": "@id"
40
+ },
41
+ "hasMember": {
42
+ "@id": "frels:hasMember",
43
+ "@type": "@id"
44
+ },
45
+ "previousVersion": "pav:previousVersion"
46
+ },
47
+ "@id": "und:xg94hm53h0c",
48
+ "bibo:eIssn": "",
49
+ "bibo:isbn": "",
50
+ "bibo:issue": "",
51
+ "bibo:numPages": "",
52
+ "bibo:pageEnd": "35",
53
+ "bibo:pageStart": "25",
54
+ "bibo:volume": "556",
55
+ "dc:abstract": "Numerical algebraic geometry is the area devoted to the solution and manipulation of polynomial systems by numerical methods, which are mainly based on continuation. Due to the extreme intrinsic parallelism of continuation, polynomial systems may be successfully dealt with that are much larger than is possible with other methods. Singular solutions require special numerical methods called endgames, and the endgames currently used do not take advantage of parallelism. This article gives an overview of continuation and endgames in the context of parallel computation. We also introduce a novel parallel algorithm for performing endgames at the end of homotopy paths, based on the Cauchy endgame, along with some heuristics useful in its implementation. This method , which has been implemented in the Bertini software package, leads to a significant gain in efficiency.",
56
+ "dc:bibliographicCitation": "Bates, D. J., Hauenstein, J. D., & Sommese, A. J. (2011). A parallel endgame. Contemp. Math, 556, 25-35.",
57
+ "dc:created": "2016-11-03",
58
+ "dc:creator#administrative_unit": "University of Notre Dame::College of Science::Applied and Computational Mathematics and Statistics",
59
+ "dc:creator#affiliation": "Faculty",
60
+ "dc:creator#author": ["Daniel Bates", "Andrew Sommese", "Jonathan Hauenstein"],
61
+ "dc:dateSubmitted": {
62
+ "@value": "2016-11-03Z",
63
+ "@type": "http://www.w3.org/2001/XMLSchema#date"
64
+ },
65
+ "dc:identifier#doi": "doi:10.7274/R0CR5R8K",
66
+ "dc:identifier#issn": "",
67
+ "dc:isPartOf": "Contemporary Mathematics",
68
+ "dc:issued": "",
69
+ "dc:language": "English",
70
+ "dc:modified": {
71
+ "@value": "2016-11-17Z",
72
+ "@type": "http://www.w3.org/2001/XMLSchema#date"
73
+ },
74
+ "dc:publisher": "American Mathematical Society",
75
+ "dc:rights": "All rights reserved",
76
+ "dc:spatial": "",
77
+ "dc:temporal": "",
78
+ "dc:title": "A Parallel Endgame",
79
+ "frels:isMemberOfCollection": {
80
+ "@id": "und:2v23vt16z2z"
81
+ },
82
+ "hydra:hasEditor": [{
83
+ "@id": "und:fq977s77m4b"
84
+ }, {
85
+ "@id": "und:ks65h99080k"
86
+ }, {
87
+ "@id": "und:v118rb69p4h"
88
+ }],
89
+ "nd:accessEdit": "jladwig,sommese,jhauenst",
90
+ "nd:accessReadGroup": "registered",
91
+ "nd:afmodel": "Article",
92
+ "nd:bendoitem": "8p58pc30d86",
93
+ "nd:depositor": "jladwig",
94
+ "nd:owner": "sommese",
95
+ "nd:representativeFile": {
96
+ "@id": "und:xk81jh36s1s"
97
+ }
98
+ }
@@ -0,0 +1,110 @@
1
+ [
2
+ {
3
+ "pid": "und:xg94hm53h0c",
4
+ "type": "fobject",
5
+ "af-model": "Article",
6
+ "rels-ext": {
7
+ "@context": {
8
+ "@vocab": "info:fedora/fedora-system:def/relations-external#",
9
+ "fedora-model": "info:fedora/fedora-system:def/model#",
10
+ "hydra": "http://projecthydra.org/ns/relations#",
11
+ "hasModel": {
12
+ "@id": "fedora-model:hasModel",
13
+ "@type": "@id"
14
+ },
15
+ "hasEditor": {
16
+ "@id": "hydra:hasEditor",
17
+ "@type": "@id"
18
+ },
19
+ "hasEditorGroup": {
20
+ "@id": "hydra:hasEditorGroup",
21
+ "@type": "@id"
22
+ },
23
+ "isPartOf": {
24
+ "@type": "@id"
25
+ },
26
+ "isMemberOfCollection": {
27
+ "@type": "@id"
28
+ },
29
+ "isEditorOf": {
30
+ "@id": "hydra:isEditorOf",
31
+ "@type": "@id"
32
+ },
33
+ "hasMember": {
34
+ "@type": "@id"
35
+ },
36
+ "previousVersion": "http://purl.org/pav/previousVersion"
37
+ },
38
+ "@id": "und:xg94hm53h0c",
39
+ "hydramata-rel:hasEditor": [
40
+ "und:fq977s77m4b",
41
+ "und:ks65h99080k",
42
+ "und:v118rb69p4h"
43
+ ],
44
+ "isMemberOfCollection": "und:2v23vt16z2z"
45
+ },
46
+ "properties-meta": {
47
+ "mime-type": "text/xml"
48
+ },
49
+ "properties": "<fields>\n<depositor>jladwig</depositor>\n<owner>sommese</owner>\n<representative>und:xk81jh36s1s</representative>\n</fields>",
50
+ "rights": {
51
+ "read-groups": [
52
+ "registered"
53
+ ],
54
+ "edit": [
55
+ "jladwig,sommese,jhauenst"
56
+ ]
57
+ },
58
+ "metadata": {
59
+ "@context": {
60
+ "bibo": "http://purl.org/ontology/bibo/",
61
+ "dc": "http://purl.org/dc/terms/",
62
+ "ebucore": "http://www.ebu.ch/metadata/ontologies/ebucore/ebucore#",
63
+ "foaf": "http://xmlns.com/foaf/0.1/",
64
+ "mrel": "http://id.loc.gov/vocabulary/relators/",
65
+ "nd": "https://library.nd.edu/ns/terms/",
66
+ "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
67
+ "vracore": "http://purl.org/vra/",
68
+ "dc:dateSubmitted": {
69
+ "@type": "http://www.w3.org/2001/XMLSchema#date"
70
+ },
71
+ "dc:created": {
72
+ "@type": "http://www.w3.org/2001/XMLSchema#date"
73
+ },
74
+ "dc:modified": {
75
+ "@type": "http://www.w3.org/2001/XMLSchema#date"
76
+ }
77
+ },
78
+ "@id": "info:fedora/und:xg94hm53h0c",
79
+ "bibo:eIssn": "",
80
+ "bibo:isbn": "",
81
+ "bibo:issue": "",
82
+ "bibo:numPages": "",
83
+ "bibo:pageEnd": "35",
84
+ "bibo:pageStart": "25",
85
+ "bibo:volume": "556",
86
+ "dc:abstract": "Numerical algebraic geometry is the area devoted to the solution and manipulation of polynomial systems by numerical methods, which are mainly based on continuation. Due to the extreme intrinsic parallelism of continuation, polynomial systems may be successfully dealt with that are much larger than is possible with other methods. Singular solutions require special numerical methods called endgames, and the endgames currently used do not take advantage of parallelism. This article gives an overview of continuation and endgames in the context of parallel computation. We also introduce a novel parallel algorithm for performing endgames at the end of homotopy paths, based on the Cauchy endgame, along with some heuristics useful in its implementation. This method , which has been implemented in the Bertini software package, leads to a significant gain in efficiency.",
87
+ "dc:bibliographicCitation": "Bates, D. J., Hauenstein, J. D., & Sommese, A. J. (2011). A parallel endgame. Contemp. Math, 556, 25-35.",
88
+ "dc:creator#administrative_unit": "University of Notre Dame::College of Science::Applied and Computational Mathematics and Statistics",
89
+ "dc:creator#affiliation": "Faculty",
90
+ "dc:creator#author": [
91
+ "Andrew Sommese",
92
+ "Jonathan Hauenstein",
93
+ "Daniel Bates"
94
+ ],
95
+ "dc:dateSubmitted": "2016-11-03Z",
96
+ "dc:identifier#doi": "doi:10.7274/R0CR5R8K",
97
+ "dc:identifier#issn": "",
98
+ "dc:isPartOf": "Contemporary Mathematics",
99
+ "dc:issued": "",
100
+ "dc:language": "English",
101
+ "dc:modified": "2016-11-17Z",
102
+ "dc:publisher": "American Mathematical Society",
103
+ "dc:rights": "All rights reserved",
104
+ "dc:spatial": "",
105
+ "dc:temporal": "",
106
+ "dc:title": "A Parallel Endgame",
107
+ "dc:created": "2016-11-03"
108
+ },
109
+ "bendo-item": "8p58pc30d86"
110
+ }]
@@ -0,0 +1,94 @@
1
+ {
2
+ "@context": {
3
+ "bibo": "http://purl.org/ontology/bibo/",
4
+ "dc": "http://purl.org/dc/terms/",
5
+ "ebucore": "http://www.ebu.ch/metadata/ontologies/ebucore/ebucore#",
6
+ "fedora-model": "info:fedora/fedora-system:def/model#",
7
+ "foaf": "http://xmlns.com/foaf/0.1/",
8
+ "frels": "info:fedora/fedora-system:def/relations-external#",
9
+ "hasEditor": {
10
+ "@id": "hydra:hasEditor",
11
+ "@type": "@id"
12
+ },
13
+ "hasEditorGroup": {
14
+ "@id": "hydra:hasEditorGroup",
15
+ "@type": "@id"
16
+ },
17
+ "hasMember": {
18
+ "@id": "frels:hasMember",
19
+ "@type": "@id"
20
+ },
21
+ "hasModel": {
22
+ "@id": "fedora-model:hasModel",
23
+ "@type": "@id"
24
+ },
25
+ "hydra": "http://projecthydra.org/ns/relations#",
26
+ "isEditorOf": {
27
+ "@id": "hydra:isEditorOf",
28
+ "@type": "@id"
29
+ },
30
+ "isMemberOfCollection": {
31
+ "@id": "frels:isMemberOfCollection",
32
+ "@type": "@id"
33
+ },
34
+ "isPartOf": {
35
+ "@id": "frels:isPartOf",
36
+ "@type": "@id"
37
+ },
38
+ "mrel": "http://id.loc.gov/vocabulary/relators/",
39
+ "ms": "http://www.ndltd.org/standards/metadata/etdms/1.1/",
40
+ "nd": "https://library.nd.edu/ns/terms/",
41
+ "pav": "http://purl.org/pav/",
42
+ "previousVersion": "pav:previousVersion",
43
+ "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
44
+ "und": "https://curate.nd.edu/show/",
45
+ "vracore": "http://purl.org/vra/"
46
+ },
47
+ "@graph": [
48
+ {
49
+ "@id": "_:b0",
50
+ "dc:contributor": "David R.Hyde",
51
+ "ms:role": "Research Director"
52
+ },
53
+ {
54
+ "@id": "_:b1",
55
+ "ms:discipline": "Biological Sciences",
56
+ "ms:level": "Doctoral Dissertation",
57
+ "ms:name": "Doctor of Philosophy"
58
+ },
59
+ {
60
+ "@id": "und:zk51vd69n1r",
61
+ "dc:contributor": {
62
+ "@id": "_:b0"
63
+ },
64
+ "dc:creator": "Jingling Li",
65
+ "dc:date": "2017-02-13",
66
+ "dc:dateSubmitted": {
67
+ "@type": "http://www.w3.org/2001/XMLSchema#date",
68
+ "@value": "2017-02-14"
69
+ },
70
+ "dc:description#abstract": "<p>The zebrafish retina provides an excellent model to study neuronal regeneration because it possesses the inherent capacity to generate new neurons in the growing retina throughout its life and to restore any neuronal types that are lost upon injury. In response to retinal cell loss caused by injury or disease, zebrafish Müller glial cells re-enter the cell cycle to produce neuronal progenitor cells that continue to proliferate and differentiate into any retinal neuronal type that was lost. We previously demonstrated that tumor necrosis factor α (TNFα) is required and sufficient to initiate this proliferation response (Nelson et al., 2013; Conner et al., 2014). However, the activation and upstream regulator of TNFα signaling during retinal regeneration remained undetermined. </p><p>In this study, I investigated the roles of two A Disintegrin And Metalloproteases 17 (ADAM17) paralogs, ADAM17a and ADAM17b, in stimulating regeneration of the damaged zebrafish retina and TNFα processing. Reduced expression of either ADAM17 paralog significantly suppressed Müller glia cell cycle re-entry in the light-damaged retina, which indicates that both ADAM17a and ADAM17b are necessary and functionally nonredundant in initiating Müller glia proliferation during retinal regeneration. The recombinant soluble TNFα rescued Müller glia proliferation in damaged <i>adam17b</i> morphant retinas, but not <i>adam17a</i> morphant retinas. We also demonstrated that knocking down ADAM17b expression reduced TNFα processing in the light-damaged retina, which results in decreased levels the soluble form of TNFα. In contrast, the <i>adam17a</i> morphant retina did not exhibit reduced amounts of the soluble TNFα. Intravitreal injection of the soluble TNFα into light-damaged retinas rescued Müller glia proliferation in <i>adam17b</i> morphant retinas, which produced proliferating neuronal progenitor cells (NPC). However, fewer NPCs in the TNFα-rescued light-damaged <i>adam17b</i> morphant retinas committed to the <i>atoh7</i> neuronal lineage relative to control retinas and differentiated into greater numbers of amacrine cells rather than photoreceptors. Thus, ADAM17b is required to process TNFα prior to Müller glia proliferation and is necessary for NPC commitment to a neuronal lineage.</p>",
71
+ "dc:modified": {
72
+ "@type": "http://www.w3.org/2001/XMLSchema#date",
73
+ "@value": "2017-02-25Z"
74
+ },
75
+ "dc:rights": "All rights reserved",
76
+ "dc:title": "Characterization of the Roles of ADAM17a and ADAM17b during Zebrafish Retinal Regeneration",
77
+ "hydra:hasEditor": {
78
+ "@id": "und:qb98mc9021z"
79
+ },
80
+ "hydra:hasEditorGroup": {
81
+ "@id": "und:q524jm23g92"
82
+ },
83
+ "ms:degree": {
84
+ "@id": "_:b1"
85
+ },
86
+ "nd:accessEdit": "curate_batch_user",
87
+ "nd:accessRead": "ljinglin",
88
+ "nd:accessReadGroup": "public",
89
+ "nd:afmodel": "Etd",
90
+ "nd:bendoitem": "zk51vd69n1r",
91
+ "nd:depositor": "curate_batch_user"
92
+ }
93
+ ]
94
+ }