-
Notifications
You must be signed in to change notification settings - Fork 24
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* changed image sizes to make them larger * added some individual page Table of Contents * fixed some image captions
- Loading branch information
1 parent
8a5b622
commit 9b90f70
Showing
10 changed files
with
72 additions
and
57 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -57,36 +57,36 @@ Please see the [video tutorial](access.html#mapper) on how to use our Map tool. | |
|
|
||
| For both the [Getty thesaurus](https://www.getty.edu/research/tools/vocabularies/tgn/) and [Google Maps](https://www.google.com/maps/) you can simply search the name of a locality, for example the Cook Strait in New Zealand. The search result on the Getty thesaurus will bring you to a page where you can obtain `decimalLatitude` and `decimalLongitdue`. | ||
|
|
||
| {width=60%} | ||
| {width=80%} | ||
|
|
||
| For Google Maps, the coordinates can be found in the url after searching. | ||
|
|
||
| {width=60%} | ||
| {width=80%} | ||
|
|
||
| ### How to use Marine Regions Gazetteer tool | ||
|
|
||
| Marine Regions offers a marine gazetteer search engine to obtain geographic information and unique identifiers for marine regions. Once you have navigated to the [gazetteer search engine](https://www.marineregions.org/gazetteer.php?p=search), you have two options to search by: enter the name of the desired locality, or enter an MRGID code. Most likely you will have a locality name but not an MRGID. You may also select a [placetype](https://www.marineregions.org/gazetteer.php?p=popup&name=placetype) to search instead for types of regions that may be physical (e.g., seamount, bay, fjord, etc.) or administrative (e.g., exclusive economic zones, countries, etc). You can specify specific sources if known (e.g., published paper, organization, etc.). Finally, you can give a latitude/longitude coordinate with a radius around it to obtain a list of regions near that point. | ||
|
|
||
| For this example we will search by geographic name for the Bay of Fundy. | ||
|
|
||
| {width=50%} | ||
| {width=60%} | ||
| {width=80%} | ||
| {width=80%} | ||
|
|
||
| Our search returned 5 results from different sources (indicated in brackets). So how do we select the correct one? We can notice right away that the second result, from SeaVox SeaArea, has a preferred alternative, which when you click on the link brings you to the IHO Sea Area description for Bay of Fundy. So already we can likely drop SeaVox as a potential candidate. A good next step may be to compare the geographical extent for each to ensure it covers the desired area. If you are uncertain about exactly where your locality is, it may be better to be safe and choose a wider geographic region. Let’s compare the maps for all 5 results: | ||
|
|
||
| {width=450%} | ||
| {width=50%} | ||
| {width=50%} | ||
| {width=50%} | ||
| {width=50%} | ||
| {width=50%} | ||
| {width=50%} | ||
| {width=50%} | ||
| {width=50%} | ||
| {width=50%} | ||
|
|
||
| Notice that no region has the exact same geographic extent. Let’s select the IHO Bay of Fundy locality (the first search result) to ensure we are covering the entire area of the Bay of Fundy, but not the Gulf. Inspecting the rest of the page, there is a lot of other useful information we can use. We can populate the following OBIS fields for our dataset, copying the information outlined in the red boxes: | ||
|
|
||
| 1. `locationID` from MRGID: <http://marineregions.org/mrgid/4289> | ||
| 2. `decimalLatitude` and `decimalLongitude` latitude and longitude coordinates of the location’s midpoint in decimal degrees: 44.97985204, -65.80601556 | ||
| 3. `coordinateUncertaintyInMeters` precision: 196726 meters | ||
|
|
||
| {width=40%} | ||
| {width=80%} | ||
|
|
||
| Since we are obtaining all this locality data from Marine Regions, we must also populate the `locationAccordingTo` field. Here, we will provide the name of the gazetteer we used to obtain the coordinates for the locality - in this case you would write “Marine Regions”. In `georeferenceRemarks` we must document that the coordinates are the region’s midpoint, that locality information was inferred by geographic name, and, where applicable, place the original locality name in the field `verbatimLocality`. Finally, the location portion of our dataset would look something like this: | ||
|
|
||
|
|
@@ -130,9 +130,9 @@ There is a new Darwin Core term [`verbatimIdentification`](https://dwc.tdwg.org/ | |
|
|
||
| The use and definitions for additional Open Nomenclature (ON) signs (`identificationQualifier`) can be found in [Open Nomenclature in the biodiversity era](https://doi.org/10.1111/2041-210X.12594), which provides examples for using the main Open Nomenclature qualifiers associated with physical specimens (Figure 1). Whereas the publication [Recommendations for the Standardisation of Open Taxonomic Nomenclature for Image-Based Identifications](https://www.frontiersin.org/articles/10.3389/fmars.2021.620702/full) provides examples and definitions for identificationQualifiers for non-physical specimens (image-based) (Figure 2). | ||
|
|
||
| .](images/fig1-openNomenclature.png){width=60%} | ||
| .*](images/fig1-openNomenclature.png){width=80%} | ||
|
|
||
| ](images/fig2-flowDiagram.jpg){width=60%} | ||
| *](images/fig2-flowDiagram.jpg){width=80%} | ||
|
|
||
| #### Changes in taxonomic classification | ||
|
|
||
|
|
@@ -171,18 +171,18 @@ Otherwise, records marked as non-marine will be dropped from the published datas | |
|
|
||
| Let’s consider an example within [this dataset](https://obis.org/dataset/9fbaeb21-a0dc-4a29-8237-1cd7ada266e0) on benthic macroalgae. Inspecting the data quality report we can see there are three dropped records due to species not being marine. | ||
|
|
||
| {width=40%} | ||
| {width=80%} | ||
|
|
||
| Clicking on the dropped records we can see which three species were dropped. By scrolling to the right of the table, we can see these records have two quality flags: NO_DEPTH and NOT_MARINE. | ||
|
|
||
| {width=40%} | ||
| {width=80%} | ||
|
|
||
| Let’s take a look at the first species, Pseudochantransia venezuelensis. When we search for this species on [WoRMS](https://www.marinespecies.org/aphia.php?p=taxdetails&id=836900) we can see that the species is marked as freshwater. | ||
|
|
||
| {width=60%} | ||
| {width=80%} | ||
|
|
||
| Cross-referencing with IRMNG, if we search for the genus-species, the species is not even found, an indication that it is not in the database (and also why it can be good to check multiple sources). Searching for just the genus, we can see that marine and brackish are stricken out, indicating the species is not marine. | ||
|
|
||
| {width=60%} | ||
| {width=80%} | ||
|
|
||
| If you have species that are marked as non-marine in these registers but are either supposed to be marine, or were found in a marine environment, then you should contact WoRMS to discuss adding it to the register. For additions and/or edits to environmental or distribution records of a species, contact the WoRMS Data Management Team at [email protected] with your request along with your record or publication substantiating the addition/change. | ||
Oops, something went wrong.