Changes
On June 9, 2023 at 8:52:29 AM UTC, Merin Reji Chacko:
-
Updated description of resource Bioinformatic Pipeline in Vertebrate and plant taxa recovered from 10 catchments in Vaud using an eDNA-metabarcoding approach to
This includes raw data, primer descriptions and the final output dataset.
-
Changed value of field
restricted
of resource Bioinformatic Pipeline to{"level":"public","allowed_users":"","shared_secret":""}
(previously{"allowed_users": "", "level": "public", "shared_secret": ""}
) in Vertebrate and plant taxa recovered from 10 catchments in Vaud using an eDNA-metabarcoding approach -
Changed value of field
resource_size
of resource Bioinformatic Pipeline to{"size_value":"4.8","size_units":"gb"}
(previously{"size_units": "gb", "size_value": "4.8"}
) in Vertebrate and plant taxa recovered from 10 catchments in Vaud using an eDNA-metabarcoding approach
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2 | "author": "[{\"affiliation\": \"WSL\", \"affiliation_02\": \"\", | 2 | "author": "[{\"affiliation\": \"WSL\", \"affiliation_02\": \"\", | ||
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4 | \"curation\", \"publication\"], \"email\": \"merin.chacko@wsl.ch\", | 4 | \"curation\", \"publication\"], \"email\": \"merin.chacko@wsl.ch\", | ||
5 | \"given_name\": \"Merin\", \"identifier\": \"0000-0002-6069-4281\", | 5 | \"given_name\": \"Merin\", \"identifier\": \"0000-0002-6069-4281\", | ||
6 | \"name\": \"Reji Chacko\"}, {\"affiliation\": \"WSL\", | 6 | \"name\": \"Reji Chacko\"}, {\"affiliation\": \"WSL\", | ||
7 | \"affiliation_02\": \"\", \"affiliation_03\": \"\", \"data_credit\": | 7 | \"affiliation_02\": \"\", \"affiliation_03\": \"\", \"data_credit\": | ||
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9 | \"fabian.fopp@wsl.ch\", \"given_name\": \"Fabian\", \"identifier\": | 9 | \"fabian.fopp@wsl.ch\", \"given_name\": \"Fabian\", \"identifier\": | ||
10 | \"0000-0003-0648-8484\", \"name\": \"Fopp\"}, {\"affiliation\": \"WSL, | 10 | \"0000-0003-0648-8484\", \"name\": \"Fopp\"}, {\"affiliation\": \"WSL, | ||
11 | ETH\", \"affiliation_02\": \"\", \"affiliation_03\": \"\", | 11 | ETH\", \"affiliation_02\": \"\", \"affiliation_03\": \"\", | ||
12 | \"data_credit\": [\"collection\", \"publication\"], \"email\": | 12 | \"data_credit\": [\"collection\", \"publication\"], \"email\": | ||
13 | \"thomas.keggin@usys.ethz.ch\", \"given_name\": \"Thomas\", | 13 | \"thomas.keggin@usys.ethz.ch\", \"given_name\": \"Thomas\", | ||
14 | \"identifier\": \"\", \"name\": \"Keggin\"}, {\"affiliation\": \"Unit | 14 | \"identifier\": \"\", \"name\": \"Keggin\"}, {\"affiliation\": \"Unit | ||
15 | of Land Change Science, Swiss Federal Research Institute WSL, | 15 | of Land Change Science, Swiss Federal Research Institute WSL, | ||
16 | Birmensdorf, Switzerland\", \"affiliation_02\": \"\", | 16 | Birmensdorf, Switzerland\", \"affiliation_02\": \"\", | ||
17 | \"affiliation_03\": \"\", \"data_credit\": [\"collection\", | 17 | \"affiliation_03\": \"\", \"data_credit\": [\"collection\", | ||
18 | \"publication\"], \"email\": \"conor.waldock@unibe.ch\", | 18 | \"publication\"], \"email\": \"conor.waldock@unibe.ch\", | ||
19 | \"given_name\": \"Conor\", \"identifier\": \"0000-0002-2818-9859\", | 19 | \"given_name\": \"Conor\", \"identifier\": \"0000-0002-2818-9859\", | ||
20 | \"name\": \"Waldock\"}, {\"affiliation\": \"WSL, ETH\", | 20 | \"name\": \"Waldock\"}, {\"affiliation\": \"WSL, ETH\", | ||
21 | \"affiliation_02\": \"\", \"affiliation_03\": \"\", \"data_credit\": | 21 | \"affiliation_02\": \"\", \"affiliation_03\": \"\", \"data_credit\": | ||
22 | [\"collection\", \"publication\"], \"email\": | 22 | [\"collection\", \"publication\"], \"email\": | ||
23 | \"eilishrichards@gmail.com\", \"given_name\": \"Eilish\", | 23 | \"eilishrichards@gmail.com\", \"given_name\": \"Eilish\", | ||
24 | \"identifier\": \"\", \"name\": \"Richards\"}, {\"affiliation\": | 24 | \"identifier\": \"\", \"name\": \"Richards\"}, {\"affiliation\": | ||
25 | \"Landscape Ecology, Institute of Terrestrial Ecosystems, ETH | 25 | \"Landscape Ecology, Institute of Terrestrial Ecosystems, ETH | ||
26 | Z\\u00fcrich, 8049 Z\\u00fcrich, Switzerland\", \"affiliation_02\": | 26 | Z\\u00fcrich, 8049 Z\\u00fcrich, Switzerland\", \"affiliation_02\": | ||
27 | \"\", \"affiliation_03\": \"\", \"data_credit\": [\"publication\", | 27 | \"\", \"affiliation_03\": \"\", \"data_credit\": [\"publication\", | ||
28 | \"supervision\"], \"email\": \"loic.pellissier@wsl.ch\", | 28 | \"supervision\"], \"email\": \"loic.pellissier@wsl.ch\", | ||
29 | \"given_name\": \"Loic\", \"identifier\": \"0000-0002-2289-8259\", | 29 | \"given_name\": \"Loic\", \"identifier\": \"0000-0002-2289-8259\", | ||
30 | \"name\": \"Pellissier\"}]", | 30 | \"name\": \"Pellissier\"}]", | ||
31 | "author_email": null, | 31 | "author_email": null, | ||
32 | "creator_user_id": "adc05669-b377-4101-b441-b9bcb92437df", | 32 | "creator_user_id": "adc05669-b377-4101-b441-b9bcb92437df", | ||
33 | "date": "[{\"date\": \"2020-06-22\", \"date_type\": \"collected\", | 33 | "date": "[{\"date\": \"2020-06-22\", \"date_type\": \"collected\", | ||
34 | \"end_date\": \"2020-06-26\"}]", | 34 | \"end_date\": \"2020-06-26\"}]", | ||
35 | "doi": "10.16904/envidat.409", | 35 | "doi": "10.16904/envidat.409", | ||
36 | "funding": "[{\"grant_number\": \"\", \"institution\": \"Swiss | 36 | "funding": "[{\"grant_number\": \"\", \"institution\": \"Swiss | ||
37 | Federal Office of the Environment (FOEN)\", \"institution_url\": | 37 | Federal Office of the Environment (FOEN)\", \"institution_url\": | ||
38 | \"https://www.bafu.admin.ch/bafu/en/home.html\"}]", | 38 | \"https://www.bafu.admin.ch/bafu/en/home.html\"}]", | ||
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41 | "isopen": true, | 41 | "isopen": true, | ||
42 | "language": "en", | 42 | "language": "en", | ||
43 | "license_id": "cc-by-sa", | 43 | "license_id": "cc-by-sa", | ||
44 | "license_title": "Creative Commons Attribution Share-Alike | 44 | "license_title": "Creative Commons Attribution Share-Alike | ||
45 | (CC-BY-SA)", | 45 | (CC-BY-SA)", | ||
46 | "license_url": "https://creativecommons.org/licenses/by-sa/4.0/", | 46 | "license_url": "https://creativecommons.org/licenses/by-sa/4.0/", | ||
47 | "maintainer": "{\"affiliation\": \"\", \"email\": | 47 | "maintainer": "{\"affiliation\": \"\", \"email\": | ||
48 | \"merin.rejichacko@gmail.com\", \"given_name\": \"Merin\", | 48 | \"merin.rejichacko@gmail.com\", \"given_name\": \"Merin\", | ||
49 | \"identifier\": \"\", \"name\": \"Reji Chacko\"}", | 49 | \"identifier\": \"\", \"name\": \"Reji Chacko\"}", | ||
50 | "maintainer_email": null, | 50 | "maintainer_email": null, | ||
51 | "metadata_created": "2023-06-06T19:26:17.207182", | 51 | "metadata_created": "2023-06-06T19:26:17.207182", | ||
n | 52 | "metadata_modified": "2023-06-09T07:18:27.508266", | n | 52 | "metadata_modified": "2023-06-09T08:52:29.265805", |
53 | "name": "catchment-biodiversity-vaud-edna", | 53 | "name": "catchment-biodiversity-vaud-edna", | ||
54 | "notes": "This dataset contains the results of a five-day field | 54 | "notes": "This dataset contains the results of a five-day field | ||
55 | excursion which the extent to which eDNA sampling can capture the | 55 | excursion which the extent to which eDNA sampling can capture the | ||
56 | diversity of a region with highly heterogeneous habitat patches across | 56 | diversity of a region with highly heterogeneous habitat patches across | ||
57 | a wide elevation gradient through multiple hydrological catchments of | 57 | a wide elevation gradient through multiple hydrological catchments of | ||
58 | the Swiss Alps. Using peristaltic pumps, we filtered 60 L of water at | 58 | the Swiss Alps. Using peristaltic pumps, we filtered 60 L of water at | ||
59 | five sites per catchment for a total volume of 1 800 L. Using an eDNA | 59 | five sites per catchment for a total volume of 1 800 L. Using an eDNA | ||
60 | metabarcoding approach focusing on vertebrates and plants, we detected | 60 | metabarcoding approach focusing on vertebrates and plants, we detected | ||
61 | 86 vertebrate taxa spanning 41 families and 263 plant taxa spanning 79 | 61 | 86 vertebrate taxa spanning 41 families and 263 plant taxa spanning 79 | ||
62 | families across ten catchments. This dataset includes two sets of | 62 | families across ten catchments. This dataset includes two sets of | ||
63 | data. The first (Bioinformatic Pipeline) includes all the steps of the | 63 | data. The first (Bioinformatic Pipeline) includes all the steps of the | ||
64 | bioinformatic pipeline, where are the second (Analysis Figures) | 64 | bioinformatic pipeline, where are the second (Analysis Figures) | ||
65 | contains tidied data and scripts for the reproduction of all | 65 | contains tidied data and scripts for the reproduction of all | ||
66 | figures/analyses in the article describing this study.", | 66 | figures/analyses in the article describing this study.", | ||
67 | "num_resources": 3, | 67 | "num_resources": 3, | ||
68 | "num_tags": 5, | 68 | "num_tags": 5, | ||
69 | "organization": { | 69 | "organization": { | ||
70 | "approval_status": "approved", | 70 | "approval_status": "approved", | ||
71 | "created": "2018-12-01T11:59:01.791513", | 71 | "created": "2018-12-01T11:59:01.791513", | ||
72 | "description": "Our laboratory aims at understanding and | 72 | "description": "Our laboratory aims at understanding and | ||
73 | forecasting the response of biodiversity to landscape changes. We | 73 | forecasting the response of biodiversity to landscape changes. We | ||
74 | investigate the historical responses of species to past changes such | 74 | investigate the historical responses of species to past changes such | ||
75 | as plate tectonics or the glaciations of the Quaternary and | 75 | as plate tectonics or the glaciations of the Quaternary and | ||
76 | contemporary responses to ongoing global changes. We develop spatial | 76 | contemporary responses to ongoing global changes. We develop spatial | ||
77 | mechanistic models of biodiversity that account for processes such as | 77 | mechanistic models of biodiversity that account for processes such as | ||
78 | dispersal and biotic interactions.", | 78 | dispersal and biotic interactions.", | ||
79 | "id": "153392ee-d556-4b16-a330-dedb177e87f9", | 79 | "id": "153392ee-d556-4b16-a330-dedb177e87f9", | ||
80 | "image_url": "2018-12-01-105921.8275952000px-LogoWSL.svg.png", | 80 | "image_url": "2018-12-01-105921.8275952000px-LogoWSL.svg.png", | ||
81 | "is_organization": true, | 81 | "is_organization": true, | ||
82 | "name": "landscape-ecology-group", | 82 | "name": "landscape-ecology-group", | ||
83 | "state": "active", | 83 | "state": "active", | ||
84 | "title": "Landscape Ecology", | 84 | "title": "Landscape Ecology", | ||
85 | "type": "organization" | 85 | "type": "organization" | ||
86 | }, | 86 | }, | ||
87 | "owner_org": "153392ee-d556-4b16-a330-dedb177e87f9", | 87 | "owner_org": "153392ee-d556-4b16-a330-dedb177e87f9", | ||
88 | "private": false, | 88 | "private": false, | ||
89 | "publication": "{\"publication_year\": \"2023\", \"publisher\": | 89 | "publication": "{\"publication_year\": \"2023\", \"publisher\": | ||
90 | \"EnviDat\"}", | 90 | \"EnviDat\"}", | ||
91 | "publication_state": "published", | 91 | "publication_state": "published", | ||
92 | "related_datasets": "Please see the publication (currently under | 92 | "related_datasets": "Please see the publication (currently under | ||
93 | revision) for a full summary of all datasets and papers associated | 93 | revision) for a full summary of all datasets and papers associated | ||
94 | with this present dataset.", | 94 | with this present dataset.", | ||
95 | "related_publications": "This dataset corrresponds to the study | 95 | "related_publications": "This dataset corrresponds to the study | ||
96 | described in the paper: Catchment-based sampling of river eDNA | 96 | described in the paper: Catchment-based sampling of river eDNA | ||
97 | integrates terrestrial and aquatic biodiversity of alpine landscapes | 97 | integrates terrestrial and aquatic biodiversity of alpine landscapes | ||
98 | (Under Revision).", | 98 | (Under Revision).", | ||
99 | "relationships_as_object": [], | 99 | "relationships_as_object": [], | ||
100 | "relationships_as_subject": [], | 100 | "relationships_as_subject": [], | ||
101 | "resource_type": "dataset", | 101 | "resource_type": "dataset", | ||
102 | "resource_type_general": "dataset", | 102 | "resource_type_general": "dataset", | ||
103 | "resources": [ | 103 | "resources": [ | ||
104 | { | 104 | { | ||
105 | "cache_last_updated": null, | 105 | "cache_last_updated": null, | ||
106 | "cache_url": null, | 106 | "cache_url": null, | ||
107 | "created": "2023-06-06T19:38:19.156383", | 107 | "created": "2023-06-06T19:38:19.156383", | ||
n | 108 | "description": "", | n | 108 | "description": "This includes raw data, primer descriptions and |
109 | the final output dataset.", | ||||
109 | "doi": "", | 110 | "doi": "", | ||
110 | "format": "ZIP", | 111 | "format": "ZIP", | ||
111 | "hash": "", | 112 | "hash": "", | ||
112 | "id": "de158722-73f9-4b69-b72b-9b9ed739705f", | 113 | "id": "de158722-73f9-4b69-b72b-9b9ed739705f", | ||
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116 | "mimetype_inner": null, | 117 | "mimetype_inner": null, | ||
117 | "name": "Bioinformatic Pipeline", | 118 | "name": "Bioinformatic Pipeline", | ||
118 | "package_id": "f1df9abc-3fb8-4253-83a8-733f712ef768", | 119 | "package_id": "f1df9abc-3fb8-4253-83a8-733f712ef768", | ||
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120 | "publication_state": "", | 121 | "publication_state": "", | ||
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123 | "resource_type": null, | 124 | "resource_type": null, | ||
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126 | "size": null, | 127 | "size": null, | ||
127 | "state": "active", | 128 | "state": "active", | ||
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130 | "url_type": null | 131 | "url_type": null | ||
131 | }, | 132 | }, | ||
132 | { | 133 | { | ||
133 | "cache_last_updated": null, | 134 | "cache_last_updated": null, | ||
134 | "cache_url": null, | 135 | "cache_url": null, | ||
135 | "created": "2023-06-06T19:52:20.702048", | 136 | "created": "2023-06-06T19:52:20.702048", | ||
136 | "description": "Information concerning the locations and times | 137 | "description": "Information concerning the locations and times | ||
137 | of sampling, as well as the identity of the samplers and relevant | 138 | of sampling, as well as the identity of the samplers and relevant | ||
138 | comments.", | 139 | comments.", | ||
139 | "doi": "", | 140 | "doi": "", | ||
140 | "format": ".csv", | 141 | "format": ".csv", | ||
141 | "hash": "", | 142 | "hash": "", | ||
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157 | "state": "active", | 158 | "state": "active", | ||
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160 | "url_type": "upload" | 161 | "url_type": "upload" | ||
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163 | "cache_last_updated": null, | 164 | "cache_last_updated": null, | ||
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165 | "created": "2023-06-06T19:53:44.269989", | 166 | "created": "2023-06-06T19:53:44.269989", | ||
166 | "description": "This zipped file includes R scripts and the | 167 | "description": "This zipped file includes R scripts and the | ||
167 | datasets required to run the analyses. A README describes the columns | 168 | datasets required to run the analyses. A README describes the columns | ||
168 | in each dataset. ", | 169 | in each dataset. ", | ||
169 | "doi": "", | 170 | "doi": "", | ||
170 | "format": ".zip", | 171 | "format": ".zip", | ||
171 | "hash": "", | 172 | "hash": "", | ||
172 | "id": "a255cdf5-9d88-4ba7-83af-df37d3c6e665", | 173 | "id": "a255cdf5-9d88-4ba7-83af-df37d3c6e665", | ||
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177 | "name": "Analysis and Figures", | 178 | "name": "Analysis and Figures", | ||
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190 | "url_type": "upload" | 191 | "url_type": "upload" | ||
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193 | "spatial": | 194 | "spatial": | ||
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195 | "spatial_info": "Switzerland", | 196 | "spatial_info": "Switzerland", | ||
196 | "state": "active", | 197 | "state": "active", | ||
197 | "subtitle": "", | 198 | "subtitle": "", | ||
198 | "tags": [ | 199 | "tags": [ | ||
199 | { | 200 | { | ||
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209 | "name": "BIOMONITORING", | 210 | "name": "BIOMONITORING", | ||
210 | "state": "active", | 211 | "state": "active", | ||
211 | "vocabulary_id": null | 212 | "vocabulary_id": null | ||
212 | }, | 213 | }, | ||
213 | { | 214 | { | ||
214 | "display_name": "DNA METABARCODING", | 215 | "display_name": "DNA METABARCODING", | ||
215 | "id": "656c05b8-489b-4f02-89b7-d57d1e295f21", | 216 | "id": "656c05b8-489b-4f02-89b7-d57d1e295f21", | ||
216 | "name": "DNA METABARCODING", | 217 | "name": "DNA METABARCODING", | ||
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219 | }, | 220 | }, | ||
220 | { | 221 | { | ||
221 | "display_name": "ENVIRONMENTAL DNA", | 222 | "display_name": "ENVIRONMENTAL DNA", | ||
222 | "id": "db7d5622-d1fc-4d24-91f7-73842c6743b6", | 223 | "id": "db7d5622-d1fc-4d24-91f7-73842c6743b6", | ||
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226 | }, | 227 | }, | ||
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228 | "display_name": "SPATIAL ECOLOGY", | 229 | "display_name": "SPATIAL ECOLOGY", | ||
229 | "id": "a3db0ef8-4bc8-48ab-93d9-23d84a6c296a", | 230 | "id": "a3db0ef8-4bc8-48ab-93d9-23d84a6c296a", | ||
230 | "name": "SPATIAL ECOLOGY", | 231 | "name": "SPATIAL ECOLOGY", | ||
231 | "state": "active", | 232 | "state": "active", | ||
232 | "vocabulary_id": null | 233 | "vocabulary_id": null | ||
233 | } | 234 | } | ||
234 | ], | 235 | ], | ||
235 | "title": "Vertebrate and plant taxa recovered from 10 catchments in | 236 | "title": "Vertebrate and plant taxa recovered from 10 catchments in | ||
236 | Vaud using an eDNA-metabarcoding approach", | 237 | Vaud using an eDNA-metabarcoding approach", | ||
237 | "type": "dataset", | 238 | "type": "dataset", | ||
238 | "url": null, | 239 | "url": null, | ||
239 | "version": "1.0" | 240 | "version": "1.0" | ||
240 | } | 241 | } |