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add FAQ, fix some formatting
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* added FAQ page
* added a page for how to map species occurrence, but it's not in bookdown yet
* fixed some header formatting to make ToC cleaner
* fixed internal link
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EliLawrence committed May 11, 2023
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74 changes: 74 additions & 0 deletions FAQ.md
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## Frequency Asked Questions

#### General

* [I have data and want to publish to OBIS - what do I do?](contribute.html)
* [Why is it important to share and format data?](contribute.html#why-publish-data-to-obis)
* [How do I handle sensitive data?](contribute.html#how-to-handle-sensitive-data)
* [I am having trouble understanding how Core and Extension tables relate to each other](relational_db.html)
* [How does the OBIS format avoid redundancy in data](relational_db.html#how-to-avoid-redundancy)
* [Where can I learn about "Darwin Core"?](darwin_core.html)
* [How are extension tables (e.g. eMOF, occurrence) linked with the core table?](formatting.html#extensions-in-obis)
* [What is the difference between Occurence Core and Event Core?](formatting.html#dataset-structure)
* [What are the responsibilities of node managers?](nodes.html)

#### Formatting Data

* [Is there a checklist of all required Darwin Core fields for OBIS?](checklist.html)
* [How does data flow in OBIS?](data_standards.html)
* [What should I do if I do not have the data for required fields by OBIS?](common_formatissues.html#missing-required-fields)
* [How do I construct an eventID?](identifiers.html#eventid)
* [How do I construct occurrenceID?](identifiers.html#occurrenceid)
* [What data goes into Occurrence core (or extension) and how do I set up this file?](format_occurrence.html)
* [How do I set up an Event core table?](format_event.html)
* [What data goes into extendedMeasurementOrFact and how do I set it up?](format_emof.html)
* [How do I map Measurement or Fact terms in OBIS with preferred BODC vocabulary?](vocabulary.html#measurementorfact-vocabularies)
* [I can't find a suitable vocabulary, how do I request a new vocabulary term?](vocabulary.html#requesting-new-vocabulary-terms)
* [How should I match raw data fields with Darwin Core terminology?](vocabulary.html#map-your-data-with-dwc-vocabulary)
* [How do I format dates?](common_formatissues.html#temporal-dates-and-times)
* [How do I handle historical data?](common_formatissues.html#historical-data)
* [How do I convert coordinates to decimal degrees?](common_formatissues.html#converting-coordinates)
* [How do I convert different geographical formats to WGS84?](common_formatissues.html#geographical-format-conversion)
* [How do I compile acoustic, imaging, or other multimedia data for OBIS?](other_data_types.html#multimedia-data-acoustic-imaging)
* [How do I compile habitat data for OBIS?](other_data_types.html#habitat-data)
* [How do I compile tracking data for OBIS?](other_data_types.html#tracking-data)
* [How do I compile DNA and genetic data for OBIS?](dna_data.html)

#### Tools

* [How do I use the WoRMS taxon match tool?](name_matching.html)
* [Can I fetch a full classification for a list of species from WoRMS?](name_matching.html#how-to-fetch-a-full-classification-for-a-list-of-species-from-worms)
* [What do I do if my scientificName does not return a match from WoRMS?](name_matching.html#what-to-do-with-non-matching-names)

#### Quality Control

* [How do I do data quality control?](data_qc.html#how-to-conduct-quality-control)
* [What are the OBIS quality control flags?]()
* [Why are certain records dropped in OBIS?](data_qc.html#why-are-records-dropped)
* What do I do when I am uncertain about the:
* [Temporal range of a dataset OR eventDate](common_qc.html#uncertain-temporal-range)
* [Geospatial location](common_qc.html#uncertain-geolocation)
* [Taxonomic identification](common_qc.html#uncertain-taxonomic-information)
* [Individual count](common_qc.html#individualcount)
* [What do I do with freshwater species that are part of my marine dataset?](common_qc.html#non-marine-species)

#### Publishing

* [How do I add my data to the OBIS database?](data_publication.html)
* [What metadata do I have to provide? Where? How?](eml.html#metadata-sections)
* [How do you know which license to choose?](data_publication.html#licenses)
* [How do I access the IPT?](ipt.html#how-to-access-the-ipt)
* [How do I use the IPT?](ipt.html#create-your-resource-on-the-ipt)
* [Are there instructions for IPT administrators?](ipt_admin.html)
* [How do I add DOI to my dataset?](data_sharing.html#adding-a-doi-to-datasets)
* [How do I publish to both GBIF and OBIS?](data_sharing.html#simultaneous-publishing-to-gbif)
* [How do I update my already published dataset?](data_sharing.html#update-your-data-in-obis)

#### Accessing data

* [How do I download data from OBIS?](access.html#obis-homepage-and-dataset-pages)
* [How can I use R to access OBIS data?](access.html#r-package)
* [How do I use the OBIS API to fetch and filter data?](access.html#api)
* [How do I contact the data provider?](access.html#api)
* [How can I cite OBIS datasets and downloads?](citing.html)
* [What are the definitions of the field names in the downloads generated by OBIS?](access.html#interpreting-downloaded-files-from-obis)
1 change: 1 addition & 0 deletions _bookdown.yml
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Expand Up @@ -5,6 +5,7 @@ rmd_files:
- index.Rmd
- policy.md
- gethelp.md
- FAQ.md
- contribute.md
- data_standards.md
- darwin_core.md
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6 changes: 3 additions & 3 deletions format_emof.md
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## How to format extendedMeasurementOrFact tables

### What data goes into eMoF
#### What data goes into eMoF

Any data related to abiotic or biotic measurements, including sampling information and protocols should be included in the eMoF table. Measurement data can also go into the [MeasurementOrFact](https://rs.gbif.org/extension/dwc/measurements_or_facts_2022-02-02.xml) extension, however OBIS recommends using the [extendedMeasurementOrFact](https://rs.gbif.org/extension/obis/extended_measurement_or_fact.xml) instead, particularly if your data is based on an Event core table.

Expand Down Expand Up @@ -38,15 +38,15 @@ Other potential fields are shown in the table below (also listed in the [checkli

*For `measurementTypeID`, `measurementUnitID`, and `measurementValueID` you must use controlled vocabulary terms. We know choosing the correct vocabulary term can be challenging, so we have provided some guidance on how to [select the correct vocabulary](vocabulary.html). It is strongly recommended to ensure these fields are filled as correctly as possible. Missing or incorrect terms will be documented in the [measurementOrFact reports](https://r.obis.org/mof/).

## How to structure eMoF
#### How to structure eMoF

Structuring data for the eMoF extension may be one of the more confusing extensions in the data formatting process. It may help to think of this extension as the table that contains all information related to any kind of measurement.

Rather than documenting each of your measurements in separate columns (e.g., columns for biomass, abundance, length, gear size, percent cover, etc.), these measurements will be condensed into one column: `measurementValue`. `measurementType` describes what the measurement actually is, for example whether it is an abundance value, length, percent cover, or any other biotic/abiotic measurement. `measurementUnit` is used to indicate the unit of the measurement.

By linking `measurementType` and `measurementValue` with the identifiers `eventID` and/or `occurrenceID`, you can have measurements linked to *one* event (e.g. temperature), measurements link to occurrence records (e.g. length), as well as sampling facts that are linked to events (size, gear, etc.). Information specifically related to how samples were taken will have the measurementTypes: `sampleSizeValue`, `sampleSizeUnit`, `samplingEffort`, and `samplingProtocol`.

### Stepwise Guidance to Format eMoF Table (in Excel)
#### Stepwise Guidance to Format eMoF Table (in Excel)

1. Create a blank sheet and name it eMoF
2. Add 9 column headers for:
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2 changes: 1 addition & 1 deletion format_event.md
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Expand Up @@ -37,7 +37,7 @@ Other terms you should consider adding are grouped by their associated Darwin Co

Terms related to measurements, either biotic (e.g., sex, lifestage) or abiotic will be included in extendedMeasurementOrFact table _not_ the Event Core or Occurrence extension table.

### Stepwise Guidance to Format Event Table (with spreadsheets)
#### Stepwise Guidance to Format Event Table (with spreadsheets)

Before proceeding with the below, make sure each record already has an [eventID](identifiers.html).

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2 changes: 1 addition & 1 deletion format_occurrence.md
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Expand Up @@ -37,7 +37,7 @@ Other terms you should consider adding are identified by their associated Darwin

Note that any terms related to measurements, either biotic (e.g., sex, lifestage, biomass) or abiotic will be included in extendedMeasurementOrFact table not the Occurrence table.

### Stepwise Guidance to Format an Occurrence Table (with spreadsheets)
#### Stepwise Guidance to Format an Occurrence Table (with spreadsheets)

Before proceeding with formatting the Occurrence table, be sure you have [completed taxon matching](name_matching.html) to obtain WoRMS LSIDs for the scientificNameID field.

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4 changes: 2 additions & 2 deletions ipt.md
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- [Introduction](#introduction-to-the-ipt)
- [How to access the IPT](#how-to-access-the-ipt)
- [Who populates IPTs?](#who-populates-the-ipt-with-datasets)
- [Upload data](#upload-data)
- [Upload data](#create-your-resource-on-the-ipt)
- [Map to Darwin Core](#map-your-data-to-darwin-core)
- [Add metadata](#add-metadata)
- [Publish on the IPT](#publish-on-the-ipt)
Expand Down Expand Up @@ -148,7 +148,7 @@ Go to your resource overview page > Metadata and click Edit to open the metadata

![Screenshot showing where to add or upload metadata](images/ipt-ss12-metadata.png){width=70%}

Follow the [OBIS metadata standards and best practices](eml.html), or check the [IPT manual](https://ipt.gbif.org/manual/en/ipt/latest/manage-resources#metadata) for detailed instructions about the metadata editor. You can also upload a file with metadata information.
Follow the guidelines on the [OBIS metadata standards and best practices](eml.html) page, or check the [IPT manual](https://ipt.gbif.org/manual/en/ipt/latest/manage-resources#metadata) for detailed instructions about the metadata editor. You can also upload a file with metadata information.

### Publish on the IPT

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23 changes: 23 additions & 0 deletions vis_map.md
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## Making maps of species in OBIS

### Mapping with the robis R package

If you’d like to visualize occurrence data using R, you can do this using the `robis` package.

After loading the installed package, let’s first fetch some occurrence data using the `occurrence` function. We will look at data for seahorses in the Genus Hippocampus.

```R
library(robis)
hippoc <- occurrence("Hippocampus")
```

We have two options for mapping:

```R
map_ggplot(hippoc)
map_leaflet(hippoc)
```

`map_ggplot` will produce a static map:

Whereas `map_leaflet` will produce an interactive leaflet map. For documentation on how to add to or change these maps (e.g.,change base map, add polygons or points, etc.), see the [Leaflet for R](https://rstudio.github.io/leaflet/).
2 changes: 1 addition & 1 deletion vocabulary.md
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Expand Up @@ -37,7 +37,7 @@ Record number, sample number, observation number | occurrenceID (either ID or in

The obistools R package also has the [map_fields function](https://github.com/iobis/obistools#map-column-names-to-darwin-core-terms) that you can use to map your dataset fields to a DwC term.

## How to correctly map eMoF terms to preferred BODC vocabulary
## How to map eMoF terms to preferred BODC vocabulary

### MeasurementOrFact vocabularies

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