Project

General

Profile

DarwinCoreArchiveScratchpads » History » Version 50

Niels Hoffmann, 11/30/2011 10:57 AM

1 1 Niels Hoffmann
2 2 Niels Hoffmann
3
4
5 12 Niels Hoffmann
# Mapping of Scratchpads data types to Darwin Core Archive
6
7
8
For a comprehensible list of DwC-A datatypes see http://tools.gbif.org/dwca-assistant/
9 2 Niels Hoffmann
10
11 44 Niels Hoffmann
Scratchpad-2.0 datatypes used for mapping, checked out from [sratchpad git repository](http://scratchpads.eu/develop) on 2011-11-23
12 30 Niels Hoffmann
13
14 33 Niels Hoffmann
This page is a work in progress.
15
16
17 2 Niels Hoffmann
{{>toc}}
18 3 Niels Hoffmann
19
20
21
22 45 Niels Hoffmann
## Core
23 1 Niels Hoffmann
24 45 Niels Hoffmann
25
### Taxonomy
26
27 40 Niels Hoffmann
| DwC-A Core | Taxon (http://rs.gbif.org/extension/dwc/identification.xml) |
28 1 Niels Hoffmann
| File | classification.txt |
29 41 Niels Hoffmann
30 45 Niels Hoffmann
#### Mapping
31 42 Niels Hoffmann
32 47 Niels Hoffmann
The Drupal module providing this data is not implemented yet for Scratchpads-2.0. The mapping here is based on the Scratchpads-1.0 implementation. 
33
34 1 Niels Hoffmann
| Table Name |	Field Name	|	Description	|	Scratchpad Comment	|	DwC-A	|	DwC-A Comment	|
35
| | | | | | |
36 47 Niels Hoffmann
| * |	field_rank_name	|	Rank	|	Select list	|	taxonRank	|	http://rs.gbif.org/vocabulary/gbif/rank.xml	|
37
| * |	field_unit_name1	|	Uninomial name, e.g. family or genus name	|	Raw text input	|	kingdom, phylum, class, order, family, genus etc.	|		|
38
| * |	field_unit_name2	|	Species epithet	|	Raw text input	|	specificEpithet	|		|
39
| * |	field_unit_name3	|	Third portion of polynomial name, e.g. subspecies name or variety	|	Raw text input	|	infraspecificEpithet	|		|
40
| * |	field_unit_name4	|	Fourth portion of polynomial name	|	Raw text input	|	[[included|in scientificName]]	|		|
41
| * |	field_unit_ind1	|	Indicator for a plant hybrid at generic level	|	Select list	|	[[included|in scientificName]][[not|in standard term set. has to be agreed upon]][[Species|Profile:isHybrid?]]	|		|
42
| * |	field_unit_ind2	|	Indicator positioned between first and second part of nam	|	Select list	|	[[included|in scientificName]][[may|be rank information]]	|		|
43
| * |	field_unit_ind3	|	Indicator positioned between second and third part of name, e.g. "spp." or "var."	|	Select list	|	[[included|in scientificName]][[is|a rank information]]	|		|
44
| * |	field_unit_ind4	|	Indicator positioned between third and fourth part of name	|	Select list	|	[[included|in scientificName]][[may|be rank information]]	|		|
45
| * |	field_usage	|	Current standing of name	|	Select list	|	taxonomicStatus	|		|
46
| * |	field_accepted_name	|	Associated Accepted Name	|	m->1 link to another taxonomy term	|	acceptedNameUsageID	|		|
47
| * |	field_unacceptability_reason	|	Unacceptability Reason	|	Select list	|	<no vocabulary yet>	|		|
48
| * |	field_taxon_author	|	Taxon author, with or without year and brackets	|	Raw text input	|	scientificNameAuthorship	|		|
49
| * |	field_reference	|	Reference	|	Select list/Autocomplete field (links to biblio content type)	|	bibliographicCitation	|		|
50
| * |	field_page_number	|	Page number	|	Raw text input	|		|		|
51
| * |	field_vernacular_name	|	Vernacular Names	|	Raw text input (one field per name)	|	vernacularName	|		|
52
* Scratchpads 2.0 table name will be filled in once the module is available.
53 4 Niels Hoffmann
54 14 Niels Hoffmann
55 4 Niels Hoffmann
----
56 1 Niels Hoffmann
57
58
59 45 Niels Hoffmann
## Extensions
60 1 Niels Hoffmann
61 45 Niels Hoffmann
62
63
### References
64
65 42 Niels Hoffmann
| DwC-A Extension | Literature Reference (http://rs.gbif.org/terms/1.0/References) |
66 49 Niels Hoffmann
| File | reference.txt |
67 1 Niels Hoffmann
68
Scratchpads relies on the [[[biblio|module](http://drupal.org/project/biblio]]) for bibliography handling.
69 26 Niels Hoffmann
70 7 Niels Hoffmann
71 1 Niels Hoffmann
For now only field that have a direct counterpart are mapped. The biblio module is much more sophisticated than DwC-A in terms of bibliography representations and it has to be decided whether custom fields should be created in DwC-A or if the excess data can be omitted. 
72 23 Niels Hoffmann
73
74 1 Niels Hoffmann
75 45 Niels Hoffmann
#### Mapping
76 41 Niels Hoffmann
77 26 Niels Hoffmann
78 31 Niels Hoffmann
| Table Name |	Field Name	|	Description	|	Scratchpad Comment	|	DwC-A	|	DwC-A Comment	|
79 5 Niels Hoffmann
| | | | | |
80 31 Niels Hoffmann
| biblio |	biblio_issn	| | |	identifier|		|
81
| biblio |	biblio_isbn	| | |	identifier	|		|
82
| biblio |	biblio_doi	| | |	identifier	|		|
83
| biblio |	biblio_accession_number	| | |	identifier	|		|
84
| biblio |	biblio_call_number	| | |	identifier	|		|
85
| biblio |	biblio_other_number	| | |	identifier	|		|
86
| biblio |	biblio_citekey	| | |	identifier	|		|
87
| |	–	| | |	bibliographicCitation	|		|
88
| node | title	|  | |	title	|		|
89
| biblio |	biblio_contributor (table)	|  ||	creator	|		|
90
| biblio |	biblio_date | | |	date	|	biblio_date should be parsed and if not possible use biblio_year; also use biblio_year when biblio_date is not provided	|
91
| biblio |	biblio_secondary_title	| | |	source	|		|
92
| biblio |	biblio_notebi	| | |	description	|		|
93
| biblio |	biblio_abst_e	| | |		|		|
94
| biblio |	biblio_custom	| | |		|		|
95
| biblio |	biblio_abst_f	| | |		|		|
96
| biblio |	biblio_notes	| | |		|		|
97
| biblio_keyword_data |	word	| | |	subject	|		|
98
| biblio |	biblio_lang	| | |	 language	|		|
99
| |		| | |	rights	|		|
100
| |		| | |	taxonRemarks	|		|
101
| biblio_types |	name	| | |	type	|	|
102
| biblio |	biblio_access_date  	| | |		|		|
103
| biblio |	biblio_alternate_title  	| | |		|		|
104
| biblio |	biblio_auth_address  	| | |		|		|
105
| biblio |	biblio_coins 	|		| | |		|
106
| biblio |	biblio_edition  	|		| | |	|
107
| biblio |	biblio_issue  	|		| | |	|
108
| biblio |	biblio_label  	|		| | |		|
109
| biblio |	biblio_md  	|		| | |		|
110
| biblio |	biblio_number_of_volumes  	| | |		|		|
111
| biblio |	biblio_number  	| | |		|		|
112
| biblio |	biblio_original_publication  	|  | |		|		|
113
| biblio |	biblio_pages  	| | |		|		|
114
| biblio |	biblio_place_published  	| |	 |	|		|
115
| biblio |	biblio_publisher  	| | |		|		|
116
| biblio |	biblio_refereed  	| | |		|		|
117
| biblio |	biblio_remote_db_name  	| |	 |	|		|
118
| biblio |	biblio_remote_db_provider  	| |	 |	|		|
119
| biblio |	biblio_repr_edition  	|		| | |		|
120
| biblio |	biblio_research_notes 	| | |		|		|
121
| biblio |	biblio_section  	|		| | |		|
122
| biblio |	biblio_short_title  	| |	 |	|		|
123 37 Niels Hoffmann
| biblio |	biblio_sort_title	|	 |for internal use in biblio |	|		|
124 31 Niels Hoffmann
| biblio |	biblio_tertiary_title  	| | |		|		|	
125
| biblio |	biblio_translated_title  	| | |		|		|
126
| biblio |	biblio_type_of_work  	| |	 |	|		|	
127
| biblio |	biblio_url  	| |	 |	|		|
128 4 Niels Hoffmann
| biblio |	biblio_volume   	| |	 |	|		|
129 1 Niels Hoffmann
130 26 Niels Hoffmann
131 1 Niels Hoffmann
132
----
133
134
135
136
### Distribution
137
138
Distribution data is based on TDWG Level 4 areas.
139 42 Niels Hoffmann
140
141
| DwC-A Extension | Species Distribution (http://rs.gbif.org/terms/1.0/Distribution) |
142 41 Niels Hoffmann
| File | distribution.txt |
143 45 Niels Hoffmann
144 26 Niels Hoffmann
145 31 Niels Hoffmann
#### Mapping
146
147 47 Niels Hoffmann
The Drupal module providing this data is not implemented yet for Scratchpads-2.0. The mapping here is based on the Scratchpads-1.0 implementation.
148 31 Niels Hoffmann
149
| Table Name |	Field Name	|	Description	|	Scratchpad Comment	|	DwC-A	|	DwC-A Comment	|
150
| | | | | | |
151 47 Niels Hoffmann
| * |	title	|	A title for the distribution – usually just the taxonomic name	|	Raw text input	|	?	|		|
152
| * |	taxonomic name	|	A link to at least one term in the taxonomy	|	Select list/Autocomplete box	|	SpeciesDistribution:coreId	|		|
153
| * |	regions	|	A list of TDWG level 4 regions	|	Select list	|	SpeciesDistribution:locationId	|	tdwg level 4 (http://rs.tdwg.org/ontology/voc/GeographicRegion.rdf)	|
154
| | ** | | | occurenceStatus | | 
155
* Scratchpads 2.0 table name will be filled in once the module is available.
156 15 Niels Hoffmann
157 47 Niels Hoffmann
  * We foresee the implementation of occurrence status in Scratchpads-2.0
158 34 Niels Hoffmann
159 1 Niels Hoffmann
160 15 Niels Hoffmann
161 4 Niels Hoffmann
----
162 14 Niels Hoffmann
163 1 Niels Hoffmann
164
165 4 Niels Hoffmann
### Images
166 42 Niels Hoffmann
167 45 Niels Hoffmann
168 1 Niels Hoffmann
  "The image data type is intended to be used to store a single image of a specimen.  The metadata associated with the image content type has therefore been designed for this purpose.  The image data type may however be used for any other image, and there will no doubt be many Scratchpads with image data objects that are not associated with a specimen." (s.rycroft)
169 26 Niels Hoffmann
170 7 Niels Hoffmann
171
| DwC-A Extension | Simple Images (http://rs.gbif.org/terms/1.0/Images) | 
172 49 Niels Hoffmann
| File | image.txt |
173 42 Niels Hoffmann
174
175 1 Niels Hoffmann
#### Mapping
176 42 Niels Hoffmann
177 47 Niels Hoffmann
The Drupal module providing this data is not implemented yet for Scratchpads-2.0. The mapping here is based on the Scratchpads-1.0 implementation.
178
179 31 Niels Hoffmann
| Table Name |	Field Name	|	Description	|	Scratchpad Comment	|	DwC-A	|	DwC-A Comment	|
180
| | | | | | |
181 47 Niels Hoffmann
| * |	title	|	A title used to reference the image	|	Raw text input	|	SimpleImage:title	|		|
182
| * |	taxonomy_N	|	A link to a term in the taxonomy	|	Select list/Autocomplete box	|	SimpleImages:[coreId]	|		|
183
| * |	taxonomy_N	|	A link to a term in the Imaging technique taxonomy	|	Select list/Autocomplete box	|	SimpleImage:format?	|		|
184
| * |	taxonomy_N	|	A link to a term in the Image galleries taxonomy	|	Select list/Autocomplete box	|	<no vocabulary yet>	|	SimpleImage does not provide a term for this kind of data. It has to be agreed upon whether this data should be omitted or, if not, which vocabulary should be used	|
185
| * |	taxonomy_N	|	A link to a term in the preparation technique taxonomy	|	Autocomplete box	|	<no vocabulary yet>	|	see above 	|
186
| * |	taxonomy_N	|	A link to a term in the keywords taxonomy	|	Autocomplete box	|	<no vocabulary yet>	|	see above	|
187
| * |	image_file	|	The image file	|	File upload	|	SimpleImage:identifier?	|		|
188
| * |	field_specimen	|	A link to a node of type specimen	|	Select list/Autocomplete box	|		|	? DwC-A is a star schema and does not allow linking other ids than the core id. Possible solutions: - use TypeAndSpecimen:occurrenceId - create two distinct DwC-A files	|
189
| * |	field_publication	|	A link to a node of type biblio	|	Select list/Autocomplete box	|		|	? DwC-A is a star schema and does not allow linking other ids than the core id	|
190
| * |	body	|	Long description of the image	|	Raw text input	|	SimpleImage:description	|		|
191 38 Niels Hoffmann
192 47 Niels Hoffmann
* Scratchpads 2.0 table name will be filled in once the module is available.
193 1 Niels Hoffmann
194
195 14 Niels Hoffmann
196
----
197 1 Niels Hoffmann
198 14 Niels Hoffmann
199 1 Niels Hoffmann
200 48 Niels Hoffmann
### Darwincore Specimen
201 43 Niels Hoffmann
202 1 Niels Hoffmann
203 48 Niels Hoffmann
  [The location and specimen data types on the Scratchpads are based on the TDWG Darwincore standard, specifically "DwC 1.2.1](http://wiki.tdwg.org/twiki/bin/view/DarwinCore/DarwinCoreVersions) (usually incorrectly refereed to as 1.21)." (s.rycroft)
204 4 Niels Hoffmann
205 1 Niels Hoffmann
206 45 Niels Hoffmann
| DwC-A Extension | Types and Specimen (http://rs.gbif.org/terms/1.0/TypesAndSpecimen) |
207 1 Niels Hoffmann
| File | typesandspecimen.txt |
208 9 Niels Hoffmann
209 50 Niels Hoffmann
210
#### Mapping
211
212
213 1 Niels Hoffmann
Mapping is self explaining.
214 11 Niels Hoffmann
215 1 Niels Hoffmann
216 7 Niels Hoffmann
217 1 Niels Hoffmann
#### Problem
218 22 Niels Hoffmann
219 1 Niels Hoffmann
220
* DwC-A is a star schema and does not allow linking other ids than the core id. **Possible solution:** Create a second DwC-A file.
221 45 Niels Hoffmann
222 1 Niels Hoffmann
223 4 Niels Hoffmann
224 18 Niels Hoffmann
----
225 1 Niels Hoffmann
226
227 42 Niels Hoffmann
228 46 Niels Hoffmann
### Taxon Description
229 26 Niels Hoffmann
230 45 Niels Hoffmann
231 47 Niels Hoffmann
  [The taxon description data type is based on the use by the Encyclopaedia of Life (EOL) of the "Species Profile Model](http://wiki.tdwg.org/SPM) (SPM).  It was originally developed to allow Scratchpad users to export descriptions from their Scratchpad, to EOL.  All of the field types are “raw text input”." (s.rycroft)
232 32 Niels Hoffmann
233 18 Niels Hoffmann
234 29 Niels Hoffmann
| DwC-A Extension | Taxon Description (http://rs.gbif.org/terms/1.0/Description) |
235 49 Niels Hoffmann
| File | description.txt |
236 4 Niels Hoffmann
237 47 Niels Hoffmann
In Scratchpads, every Taxon Description type is stored in a distinct table. In order to make the mapping more clear we divided the fields into two tables. Table "Scratchpad Taxon Description Names" holds the description types and their according table names in the Drupal database. Every entry in Table "Scratchpad Taxon Description Names" will map to DwC-A as described by Table "Mapping".
238 4 Niels Hoffmann
239 1 Niels Hoffmann
240 39 Niels Hoffmann
241 18 Niels Hoffmann
#### Scratchpad Taxon Description Names
242
243 1 Niels Hoffmann
244
|	Name	|	Table name |    Description	|
245
| | | |
246 47 Niels Hoffmann
|	Overview	| * |	Primary chapter heading in the Encyclopedia of Life.	|
247 1 Niels Hoffmann
|	General Description	| field_data_field_general_description |	A comprehensive description of the characteristics of the taxon. To be used primarily when many of the subject categories are treated together in one object, but at length. Taxon biology is to be used if a brief summary.	|
248
|	Biology	| field_data_field_biology |	An account of the biology of the taxon. E.g. behavior, reproduction, dispersal.	|
249 47 Niels Hoffmann
|	Conservation	| * |	Primary chapter heading in the Encyclopedia of Life.	|
250 1 Niels Hoffmann
|	Conservation Status	| field_data_field_conservation_status |	A description of the likelihood of the species becoming extinct in the present day or in the near future. Population size is treated under Population Biology, and trends in population sizes are treated under Trends. However, this is the preferred element if an object includes all of these things and details about conservation listings.	|
251
|	Legislation	| field_data_field_legislations |	Legal regulations or statutes relating to the taxon.	|
252 32 Niels Hoffmann
|	Management	| field_data_field_management |	Describes techniques and goals used in management of species. May include management relative to a piece of legislation, e.g., a CITES list. [[this|is a change in the intent and will need to be considered by TDWG]]	|
253 18 Niels Hoffmann
|	Procedures	| field_data_field_procedures |	Deals with how you go about managing this taxon; what are the known threats to this taxon?	|
254 24 Niels Hoffmann
|	Threats	| field_data_field_threats |	The threats to which this taxon is subject.	|
255 18 Niels Hoffmann
|	Trends	| field_data_field_trends |	An indication of whether a population is stable, or increasing or decreasing.	|
256 47 Niels Hoffmann
|	Description	| * |	Primary chapter heading in the Encyclopedia of Life.	|
257 24 Niels Hoffmann
|	Behaviour	| field_data_field_behavious |	Description of behaviour and behaviour patterns of an organism, including actions and reactions of organism in relation to its biotic and abiotic environment. Includes communication, perception, modes and mechanisms of locomotion, as well as long term strategies (except mating and reproductive strategies, covered under reproduction).	|
258 18 Niels Hoffmann
|	Cytology	| field_data_field_cytology |	Cell biology: formation, structure, organelles, and function of cells.	|
259
|	Diagnostic Description	| field_data_field_diagnostic_description |	Lists the features that distinguish this taxon from its closest relatives. May include but is not restricted to synapomorphies.	|
260
|	Genetics	| field_data_field_genetics |	Information on the genetics of the taxon, including karyotypes, barcoding status, whole genome sequencing status, ploidy.	|
261
|	Growth	| field_data_field_growth |	Description of growth rates, allometries, parameters known to be predictive, morphometrics. Can also include hypotheses of paedomorphy or neoteny, etc.	|
262
|	Look Alikes	| field_data_field_look_alikes |	Other taxa that this taxon may be confused with. Useful for identification and comparison. Common in invasive species communities.	|
263
|	Molecular Biology	| field_data_field_molecular_biology |	Includes proteomic and biochemistry (e.g Toxicity). Genomic information is usually treated under genetics.	|
264 24 Niels Hoffmann
|	Morphology	| field_data_field_morphology |	Description of the appearance of the taxon; e.g body plan, shape and color of external features, typical postures. May be referred to as or include habit, or anatomy.	|
265 18 Niels Hoffmann
|	Physiology	| field_data_field_physiology |	Description of physiological processes. Includes metabolic rates, and systems such as circulation, respiration, excretion, immunity, neurophysiology.	|
266
|	Size	| field_data_field_size |	Average size, max, range; type of size (perimeter, length, volume, weight ...)	|
267
|	Taxon Biology	| field_data_field_taxon_biology |	Summary or overview of all aspects of an organism's biology. [[this|may be a change in intent and need to be reviewed by TDWG]]	|
268 47 Niels Hoffmann
|	Ecology and Distribution	| * |	Primary chapter heading in the Encyclopedia of Life.	|
269 18 Niels Hoffmann
|	Associations	| field_data_field_associations |	Descriptions and lists of taxa that interact with the subject taxon. Includes explicit reference to the kind of ecological interaction: Predator/prey; host/parasite, pollinators, symbiosis, mutualism, commensalism; hybridisation, …	|
270
|	Cyclicity	| field_data_field_cyclicity |	Description of biorhythms, whether on the scale of seconds, hours, days, or seasons. Those states or conditions characterised by regular repetition in time. Could also cover phenomena such as chewing rates. Life cycles are treated in the Life Cycle term. Seasonal migration and reproduction are usually treated separately.	|
271
|	Dispersal	| field_data_field_dispersal |	Description of the methods, circumstances, and timing of dispersal (includes both natal dispersal and interbreeding dispersal?)	|
272
|	Distribution	| field_data_field_distribution |	Covers ranges, e.g., a global range, or a narrower one; may be biogeographical, political or other (e.g., managed areas like conservencies); endemism; native or exotic; ref Darwin Core Geospatial extension. Does not include altitudinal distribution.	|
273
|	Ecology	| field_data_field_ecology |	Ecology	|
274
|	Habitat	|	 field_data_field_habitat |Includes realm (e.g Terrestrial etc) and climatic information (e.g Boreal); also includes requirements and tolerances; horizontal and vertical (altitudinal) distribution.	|
275
|	Life Cycle	|	 field_data_field_life_cycle |Defines and describes obligatory developmental transformations. Includes metamorphosis, instars, gametophyte/embryophytes, transitions from sessile to mobile forms. Discusses timing. Morphology usually described in morphological descriptions.	|
276 24 Niels Hoffmann
|	Life Expectancy	| field_data_field_life_expectancy |	Any information on longevity, including The average period an organism can be expected to survive.	|
277 18 Niels Hoffmann
|	Migration	| field_data_field_migration |	Description of the periodic movement of organisms from one locality to another (e.g., for breeding). Usually includes locality, timing, and hypothesized purpose.	|
278 1 Niels Hoffmann
|	Trophic Strategy	|	 field_data_field_trophic_strategy |Summaries general nature of feeding interactions. For example, basic mode of nutrient uptake (autotrophy, heterotrophy, coprophagy, saprophagy), position in food network (top predator, primary producer, consumer), diet categorization (detritovore, omnivore, carnivore, herbivore). Specific lists of taxa are treated under associations (specifying predators or prey).	|
279 18 Niels Hoffmann
|	Population Biology	| field_data_field_population_biology |	Includes abundance information (population size, density) and demographics (e.g. age stratification).	|
280
|	Reproduction	| field_data_field_reproduction |	Description of reproductive physiology and behavior, including mating and life history variables. Includes cues, strategies, restraints, rates.	|
281 48 Niels Hoffmann
|	Evolution and Systematics	| * |	Primary chapter heading in the Encyclopedia of Life	|
282 18 Niels Hoffmann
|	Evolution	| field_data_field_evolution |	Description of the evolution of the taxon.	|
283
|	Phylogeny	| field_data_field_phylogeny |	Description of phylogenetic and systematic treatments of the taxon.	|
284 47 Niels Hoffmann
|	Relevance	| * |	Primary chapter heading in the Encyclopedia of Life.	|
285 18 Niels Hoffmann
|	Diseases	| field_data_field_diseaeses |	Description of diseases that the organism is subject to. Disease-causing organisms can also be listed under associations.	|
286
|	Risk Statement	| field_data_field_risk_statement |	Negative impacts on humans, communities. [[This|may also include impacts on ecosystems should the organism decline or be extirpated -- this is probably a change in intent from TDWG]]	|
287
|	Uses	| field_data_field_uses |	Benefits for humans. ref Cook "Economic Botany" Can include ecosystem services. However, benefits to ecosystems not specific to humans are best treated under Risk statement (what happens when the organism is removed)	|
288
289 24 Niels Hoffmann
* These fields merely represent chapter headings and do not contain relvant data.
290 1 Niels Hoffmann
291 47 Niels Hoffmann
292
293
294
#### Mapping
295
296
|	Table name	| Field name	|	Dwc-A	|	Description	|
297
|		|		|		|		|
298
|	<!ScratchpadTaxonDescriptionName.TableName>	| 	|	type	|	Overview, General Description, Biology etc.	|
299
|	<!ScratchpadTaxonDescriptionName.TableName> |	field_<!ScratchpadTaxonDescriptionName>_value	|	description	|	free text 	|
300
301 14 Niels Hoffmann
302
303
304 1 Niels Hoffmann
----