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Mapping of Scratchpads data types to Darwin Core Archive

For a comprehensible list of DwC-A datatypes see http://tools.gbif.org/dwca-assistant/

Scratchpad-2.0 datatypes used for mapping, checked out from sratchpad git repository on 2011-11-23

This page is a work in progress.

Core

Taxonomy

| DwC-A Core | Taxon (http://rs.gbif.org/extension/dwc/identification.xml) |
| File | classification.txt |

Mapping

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.

| Table Name | Field Name | Description | Scratchpad Comment | DwC-A | DwC-A Comment |
| | | | | | |
| * | field_rank_name | Rank | Select list | taxonRank | http://rs.gbif.org/vocabulary/gbif/rank.xml |
| * | field_unit_name1 | Uninomial name, e.g. family or genus name | Raw text input | kingdom, phylum, class, order, family, genus etc. | |
| * | field_unit_name2 | Species epithet | Raw text input | specificEpithet | |
| * | field_unit_name3 | Third portion of polynomial name, e.g. subspecies name or variety | Raw text input | infraspecificEpithet | |
| * | field_unit_name4 | Fourth portion of polynomial name | Raw text input | in scientificName | |
| * | field_unit_ind1 | Indicator for a plant hybrid at generic level | Select list | in scientificNamein standard term set. has to be agreed uponProfile:isHybrid? | |
| * | field_unit_ind2 | Indicator positioned between first and second part of nam | Select list | in scientificNamebe rank information | |
| * | field_unit_ind3 | Indicator positioned between second and third part of name, e.g. "spp." or "var." | Select list | in scientificNamea rank information | |
| * | field_unit_ind4 | Indicator positioned between third and fourth part of name | Select list | in scientificNamebe rank information | |
| * | field_usage | Current standing of name | Select list | taxonomicStatus | |
| * | field_accepted_name | Associated Accepted Name | m->1 link to another taxonomy term | acceptedNameUsageID | |
| * | field_unacceptability_reason | Unacceptability Reason | Select list | | |
| * | field_taxon_author | Taxon author, with or without year and brackets | Raw text input | scientificNameAuthorship | |
| * | field_reference | Reference | Select list/Autocomplete field (links to biblio content type) | bibliographicCitation | |
| * | field_page_number | Page number | Raw text input | | |
| * | field_vernacular_name | Vernacular Names | Raw text input (one field per name) | vernacularName | |
* Scratchpads 2.0 table name will be filled in once the module is available.


Extensions

References

| DwC-A Extension | Literature Reference (http://rs.gbif.org/terms/1.0/References) |
| File | reference.txt |

Scratchpads relies on the [[[biblio|module](http://drupal.org/project/biblio]]) for bibliography handling.

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.

Mapping

| Table Name | Field Name | Description | Scratchpad Comment | DwC-A | DwC-A Comment |
| | | | | |
| biblio | biblio_issn | | | identifier| |
| biblio | biblio_isbn | | | identifier | |
| biblio | biblio_doi | | | identifier | |
| biblio | biblio_accession_number | | | identifier | |
| biblio | biblio_call_number | | | identifier | |
| biblio | biblio_other_number | | | identifier | |
| biblio | biblio_citekey | | | identifier | |
| | – | | | bibliographicCitation | |
| node | title | | | title | |
| biblio | biblio_contributor (table) | || creator | |
| 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 |
| biblio | biblio_secondary_title | | | source | |
| biblio | biblio_notebi | | | description | |
| biblio | biblio_abst_e | | | | |
| biblio | biblio_custom | | | | |
| biblio | biblio_abst_f | | | | |
| biblio | biblio_notes | | | | |
| biblio_keyword_data | word | | | subject | |
| biblio | biblio_lang | | | language | |
| | | | | rights | |
| | | | | taxonRemarks | |
| biblio_types | name | | | type | |
| biblio | biblio_access_date | | | | |
| biblio | biblio_alternate_title | | | | |
| biblio | biblio_auth_address | | | | |
| biblio | biblio_coins | | | | |
| biblio | biblio_edition | | | | |
| biblio | biblio_issue | | | | |
| biblio | biblio_label | | | | |
| biblio | biblio_md | | | | |
| biblio | biblio_number_of_volumes | | | | |
| biblio | biblio_number | | | | |
| biblio | biblio_original_publication | | | | |
| biblio | biblio_pages | | | | |
| biblio | biblio_place_published | | | | |
| biblio | biblio_publisher | | | | |
| biblio | biblio_refereed | | | | |
| biblio | biblio_remote_db_name | | | | |
| biblio | biblio_remote_db_provider | | | | |
| biblio | biblio_repr_edition | | | | |
| biblio | biblio_research_notes | | | | |
| biblio | biblio_section | | | | |
| biblio | biblio_short_title | | | | |
| biblio | biblio_sort_title | |for internal use in biblio | | |
| biblio | biblio_tertiary_title | | | | |

| biblio | biblio_translated_title | | | | |
| biblio | biblio_type_of_work | | | | |

| biblio | biblio_url | | | | |
| biblio | biblio_volume | | | | |


Distribution

Distribution data is based on TDWG Level 4 areas.

| DwC-A Extension | Species Distribution (http://rs.gbif.org/terms/1.0/Distribution) |
| File | distribution.txt |

Mapping

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.

| Table Name | Field Name | Description | Scratchpad Comment | DwC-A | DwC-A Comment |
| | | | | | |
| * | title | A title for the distribution – usually just the taxonomic name | Raw text input | ? | |
| * | taxonomic name | A link to at least one term in the taxonomy | Select list/Autocomplete box | SpeciesDistribution:coreId | |
| * | regions | A list of TDWG level 4 regions | Select list | SpeciesDistribution:locationId | tdwg level 4 (http://rs.tdwg.org/ontology/voc/GeographicRegion.rdf) |
| | ** | | | occurenceStatus | |
* Scratchpads 2.0 table name will be filled in once the module is available.

  • We foresee the implementation of occurrence status in Scratchpads-2.0

Images

"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)

| DwC-A Extension | Simple Images (http://rs.gbif.org/terms/1.0/Images) | 
| File | image.txt |

Mapping

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.

| Table Name | Field Name | Description | Scratchpad Comment | DwC-A | DwC-A Comment |
| | | | | | |
| * | title | A title used to reference the image | Raw text input | SimpleImage:title | |
| * | taxonomy_N | A link to a term in the taxonomy | Select list/Autocomplete box | SimpleImages:[coreId] | |
| * | taxonomy_N | A link to a term in the Imaging technique taxonomy | Select list/Autocomplete box | SimpleImage:format? | |
| * | taxonomy_N | A link to a term in the Image galleries taxonomy | Select list/Autocomplete box | | 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 |
| * | taxonomy_N | A link to a term in the preparation technique taxonomy | Autocomplete box | | see above |
| * | taxonomy_N | A link to a term in the keywords taxonomy | Autocomplete box | | see above |
| * | image_file | The image file | File upload | SimpleImage:identifier? | |
| * | 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 |
| * | 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 |
| * | body | Long description of the image | Raw text input | SimpleImage:description | |

  • Scratchpads 2.0 table name will be filled in once the module is available.

Darwincore Specimen

The location and specimen data types on the Scratchpads are based on the TDWG Darwincore standard, specifically "DwC 1.2.1 (usually incorrectly refereed to as 1.21)." (s.rycroft)

| DwC-A Extension | Types and Specimen (http://rs.gbif.org/terms/1.0/TypesAndSpecimen) |
| File | typesandspecimen.txt |

Mapping

Mapping is self explaining.

Problem

  • 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.

Taxon Description

The taxon description data type is based on the use by the Encyclopaedia of Life (EOL) of the "Species Profile Model (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)

| DwC-A Extension | Taxon Description (http://rs.gbif.org/terms/1.0/Description) |
| File | description.txt |

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".

Scratchpad Taxon Description Names

| Name | Table name | Description |
| | | |
| Overview | * | Primary chapter heading in the Encyclopedia of Life. |
| 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. |
| Biology | field_data_field_biology | An account of the biology of the taxon. E.g. behavior, reproduction, dispersal. |
| Conservation | * | Primary chapter heading in the Encyclopedia of Life. |
| 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. |
| Legislation | field_data_field_legislations | Legal regulations or statutes relating to the taxon. |
| 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. is a change in the intent and will need to be considered by TDWG |
| Procedures | field_data_field_procedures | Deals with how you go about managing this taxon; what are the known threats to this taxon? |
| Threats | field_data_field_threats | The threats to which this taxon is subject. |
| Trends | field_data_field_trends | An indication of whether a population is stable, or increasing or decreasing. |
| Description | * | Primary chapter heading in the Encyclopedia of Life. |
| 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). |
| Cytology | field_data_field_cytology | Cell biology: formation, structure, organelles, and function of cells. |
| 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. |
| Genetics | field_data_field_genetics | Information on the genetics of the taxon, including karyotypes, barcoding status, whole genome sequencing status, ploidy. |
| 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. |
| 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. |
| Molecular Biology | field_data_field_molecular_biology | Includes proteomic and biochemistry (e.g Toxicity). Genomic information is usually treated under genetics. |
| 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. |
| Physiology | field_data_field_physiology | Description of physiological processes. Includes metabolic rates, and systems such as circulation, respiration, excretion, immunity, neurophysiology. |
| Size | field_data_field_size | Average size, max, range; type of size (perimeter, length, volume, weight ...) |
| Taxon Biology | field_data_field_taxon_biology | Summary or overview of all aspects of an organism's biology. may be a change in intent and need to be reviewed by TDWG |
| Ecology and Distribution | * | Primary chapter heading in the Encyclopedia of Life. |
| 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, … |
| 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. |
| Dispersal | field_data_field_dispersal | Description of the methods, circumstances, and timing of dispersal (includes both natal dispersal and interbreeding dispersal?) |
| 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. |
| Ecology | field_data_field_ecology | Ecology |
| 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. |
| 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. |
| Life Expectancy | field_data_field_life_expectancy | Any information on longevity, including The average period an organism can be expected to survive. |
| 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. |
| 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). |
| Population Biology | field_data_field_population_biology | Includes abundance information (population size, density) and demographics (e.g. age stratification). |
| Reproduction | field_data_field_reproduction | Description of reproductive physiology and behavior, including mating and life history variables. Includes cues, strategies, restraints, rates. |
| Evolution and Systematics | * | Primary chapter heading in the Encyclopedia of Life |
| Evolution | field_data_field_evolution | Description of the evolution of the taxon. |
| Phylogeny | field_data_field_phylogeny | Description of phylogenetic and systematic treatments of the taxon. |
| Relevance | * | Primary chapter heading in the Encyclopedia of Life. |
| Diseases | field_data_field_diseaeses | Description of diseases that the organism is subject to. Disease-causing organisms can also be listed under associations. |
| Risk Statement | field_data_field_risk_statement | Negative impacts on humans, communities. may also include impacts on ecosystems should the organism decline or be extirpated -- this is probably a change in intent from TDWG |
| 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) |

  • These fields merely represent chapter headings and do not contain relvant data.

Mapping

| Table name | Field name | Dwc-A | Description |
| | | | |
| <!ScratchpadTaxonDescriptionName.TableName> | | type | Overview, General Description, Biology etc. |
| <!ScratchpadTaxonDescriptionName.TableName> | field_<!ScratchpadTaxonDescriptionName>_value | description | free text |


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