====== Digitization of SMNSs Collections ======


FIXME 
====== Definition ======

Digitization at ZFMK: implementation and maintenance of a **Digital Collection Catalogue** (DCC).

The Catalogue contains all the information from the collections objoects, annotated with information about Places, Persons, Literature, and related research data (e.g. genetic barcodes).

====== Infratructure ======

An infrastructure is setup for the implementation of the DCC consisting of:


  * [[dwb:overview| Diversity Workbench framework]]
  * [[d_a_m:overview| Digital Asset Management System]] FIXME
  * [[biodivinf:digitization:portal| Digital Collection Portal]]
  * [[biodivinf:digitization:statistics| Digitization Statistics]]
  * [[biocase:overview| BioCASe Provider Software]]
  * [[biodivinf:digitization:material| Equipment for Digititization]]
  * [[biodivinf:digitization:withhold| Withhold demands]]
  * [[biodivinf:digitization:versioning| Versioning]]

===== Some Links =====

  ; ICDIG : [[https://icedig.eu/content/deliverables|Deliverables]]
  ; WeDigBio : [[https://wedigbio.org/|Worldwide Engagement for Digitizing Biocollections]]
  
===== Rationale: =====

Practical challenges for researchers in data sharing: https://figshare.com/articles/Infographic_-_Practical_challenges_for_researchers_in_data_sharing/5996786

The Fourth Paradigm: Data-Intensive Scientific Discovery 
(https://www.microsoft.com/en-us/research/publication/fourth-paradigm-data-intensive-scientific-discovery/)

  - "eScience is where IT meets scientists" (Fourth Paradigm) page XViX, fig. 2
  - empirical science -> machine supported data exploration  
  - Hauptproblem: Erfassung einfacher als Kuration (Jim Grey) page xiii-xiv, xx

===== Images =====


  * Images in: P:\CollDig\<Section name>\Bilder. Create a subdirectory per Taxon.
  * Recommended image format is TIF. Resolution should be 300 dpi at a minimum for A4 size. 
  * Image name: collectionnumber_running number
  * Color-Depth should be 8 bit. Images that are going to be used in a scientific context, e.g. CT scans or histological images can have 16 bit.

  * [[https://physalia.evolution.uni-bonn.de/dzviewer/index.html?imageURL=https://physalia.evolution.uni-bonn.de/dumping/ZFMK/ZFMK_53.jpg|DeepZoom-Viewer]]
  * Current development in GFBio: https://gfbio.biowikifarm.net/internal/Subtask_5.4.3:_Support_for_multimedia_data


===== Person names =====

  ; VIAF :  http://viaf.org/viaf/partnerpages/DNB.html
  ; DNB : https://portal.dnb.de/opac.htm?query=per%3D%22M%C3%BCller%2C+Johann+Friedrich+Theodor%22+sortBy+ka%2Fsort.ascending&method=simpleSearch&cqlMode=true => Eintragen der ID in URL Feld: http://d-nb.info/gnd/118737457

===== Taxon Names =====


[[https://bdj.pensoft.net/articles.php?id=9787&instance_id=3338935 | Taxonaut: an application software for comparative display of multiple taxonomies with a use case of GBIF Species API]]

[[https://www.gbif-uat.org/developer/species|GBIF Species API]]
===== Data Quality =====

==== Sampling-event datasets ====

Taken from: http://bid.gbif.org/en/community/data-quality/#sampling

Learn more about sampling-event and other classes of datasets currently supported on GBIF.org
Darwin Core record details

  ;  //Term// : //Status//
  ;  eventID : Required
  ;  eventDate : Required
  ;  countryCode : Required
  ;  samplingProtocol : Required
  ;  samplingSizeValue & samplingSizeUnit : Required
  ;  parentEventID : Strongly recommended
  ;  samplingEffort : Strongly recommended
  ;  locationID : Strongly recommended
  ;  decimalLatitude & decimalLongitude2 : Strongly recommended
  ;  geodeticDatum : Strongly recommended
  ;  coordinateUncertaintyInMeters : Strongly recommended
  ;  footprintWKT : Strongly recommended
  ;  occurrenceStatus : Strongly recommended



FIXME
I (Björn) am quite unsure with this kind of recommendations because of:
  * As long as we do (can) not provide an easy to use infrastructure for external IDs it is not applicable to provide locationIDs, parentEventIDs, eventIDs. There is a real danger we are collect a hay stack of private IDs that can never be resolved to events, locations etc. It will be much better to set up a small set of relevant Event parameters that must be provided in an standardized form: Time, Location in WGS 84 coordinates, Names and Institutions of involved persons
  * The [[http://tdwg.github.io/dwc/terms/index.htm|Darwin Core Reference Guide]] provides vague example texts and examples for external references but neither a real vocabulary nor a data model
  * There are no applicable standard for defining efforts of sampling, most of these informations will be irrelevant because other researchers are in complete different situations when doing their own research  
  * footprintWKT would recommend that our users know WKT
  * occurrenceStatus is present or absent, does not provide any relevant information when we deal with collected specimens, but would be relevant for ecological or occurrence studies
  * The recommendations are not sufficient for ecological or occurrence studies