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* added content to dataset structure (cores & extensions)
* restructured examples page so dna data and special data types are separate pages. added some content here too
* attempting to fix image code so they will load!!
* added rest of rows for checklist
* altering node page
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EliLawrence committed Mar 7, 2023
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2 changes: 2 additions & 0 deletions _bookdown.yml
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- vocabulary.md
- common_formatissues.md
- examples.md
- dna_data.md
- other_data_types.md
- data_qc.md
- mofreports.md
- dataquality.md
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240 changes: 207 additions & 33 deletions checklist.md

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17 changes: 2 additions & 15 deletions data_format.md
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##### eDNA & DNA derived data Extension

DNA derived data are increasingly being used to document taxon occurrences. To ensure these data are useful to the broadest possible community, GBIF published a guide entitled [Publishing DNA-derived data through biodiversity data platforms](https://docs.gbif-uat.org/publishing-dna-derived-data/1.0/en/). This guide is supported by the DNA derived data extension for Darwin Core, which incorporates MIxS terms into the Darwin Core standard. eDNA and DNA derived data is linked to occurrence data with the use of `occurrenceID` and/ or `eventID`. Refer to the [Examples: ENV-DATA and DNA derived data](examples#edna-dna-derived-data.html) for use case examples of eDNA and DNA derived data.
DNA derived data are increasingly being used to document taxon occurrences. To ensure these data are useful to the broadest possible community, GBIF published a guide entitled [Publishing DNA-derived data through biodiversity data platforms](https://docs.gbif-uat.org/publishing-dna-derived-data/1.0/en/). This guide is supported by the DNA derived data extension for Darwin Core, which incorporates MIxS terms into the Darwin Core standard. eDNA and DNA derived data is linked to occurrence data with the use of `occurrenceID` and/ or `eventID`. Refer to the [Examples: ENV-DATA and DNA derived data](dna_data.html) for use case examples of eDNA and DNA derived data.

##### A special case: habitat types

Event Core is perfect for enriching OBIS with interpreted information such as biological community, biotope or habitat type (collectively referred to as 'habitats'). However, the unconstrained nature of the terms `measurementTypeID`, `measurementValueID`, and `measurementUnitID` leads to a risk that habitats measurements are structured inconsistently within the Darwin Core Archive standard and as a result, are not easily discoverable, understood or usable.

As a result, members of the European Marine Observation and Data Network (EMODnet) Seabed Habitats and Biology thematic groups have produced a document [Duncan et al. (2021)](https://www.emodnet-seabedhabitats.eu/resources/documents-and-outreach/#h3298bcd0a15741a8a0ac1c8b4576f7c5) that recommends a consistent approach to structuring classified habitat data in Europe using the Darwin Core eMoF Extension. Note that this approach has not yet been discussed or approved at the global level so the implementation at the EurOBIS level may be considered a pilot.

The overarching principles are summarised here. Note that because of the numerous classification systems and priority habitat lists in existence, it is not possible to point to a single vocabulary for populating each of `measurementTypeID`, `measurementValueID` and `measurementUnitID`, as for other measurement types, so below are the *types* of information to include, with an example, as recommended by [Duncan et al. (2021)](https://www.emodnet-seabedhabitats.eu/resources/documents-and-outreach/#h3298bcd0a15741a8a0ac1c8b4576f7c5):

- `measurementTypeID`: A machine-readable URI or DOI reference describing the (version of the) classification system itself. For example: [https://dd.eionet.europa.eu/vocabulary/biodiversity/eunishabitats/](https://dd.eionet.europa.eu/vocabulary/biodiversity/eunishabitats/)
- `measurementValueID`: If available, a machine-readable URI describing the habitat class in “measurementValue”. For example: [https://dd.eionet.europa.eu/vocabulary/biodiversity/eunishabitats/A5.36](https://dd.eionet.europa.eu/vocabulary/biodiversity/eunishabitats/A5.36)
- `measurementUnitID`: null because habitat types are unitless.

Please consult [Duncan et al. (2021)](https://www.emodnet-seabedhabitats.eu/resources/documents-and-outreach/#h3298bcd0a15741a8a0ac1c8b4576f7c5) for more details, including:
- how to handle a single event with multiple habitat measurements
- recommended vocabularies and terms for common habitat classification systems
- example eMoF table
Including information on habitats (biological community, biotope, or habitat type) is possible and encouraged with the use of Event Core. However, beware the unconstrained nature of the terms `measurementTypeID`, `measurementValueID`, and `measurementUnitID` which can lead to inconsistently documented habitat measurements within the Darwin Core Archive standard. To ensure this data is more easily discoverable, understood or usable, refer to [Examples: habitat data](other_data_types#habitat-data.html) and/or [Duncan et al. (2021)](https://www.emodnet-seabedhabitats.eu/resources/documents-and-outreach/#h3298bcd0a15741a8a0ac1c8b4576f7c5) for use case examples and more details.

##### Recommended reading

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2 changes: 1 addition & 1 deletion data_standards.md
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## OBIS Data Life Cycle

<img src="images/OBISdataLifeCycle.png" class="img-responsive" display: inline-block />
<img src="images/OBISdataLifeCycle.png" class="img-responsive" display: inline-block/>

The basic data life cycle for contributions to OBIS can be broken down into six step-by-step phases:

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