diff --git a/access.md b/access.md index 349cba2..ed0427a 100644 --- a/access.md +++ b/access.md @@ -83,7 +83,7 @@ From the OBIS homepage, you can search for data in the search bar in the middle When you search by dataset you will notice an additional option appears for [advanced search options](https://obis.org/datasets). This will allow you to identify specific datasets, and apply filters for OBIS nodes and whether datasets include extensions. -![*OBIS homepage search, showing where to find the advanced search link*](images/obis-homepagesearch.png){width=70%} +![*OBIS homepage search, showing where to find the advanced search link*](images/obis-homepagesearch.png){width=90%} Regardless if you found a dataset through the homepage or the advanced Dataset search, you will be able to navigate to individual dataset pages. For individual dataset pages (instead of aggregate pages for e.g., a Family) there are three buttons available: @@ -91,7 +91,7 @@ Regardless if you found a dataset through the homepage or the advanced Dataset s * Source DwC-A - download the dataset as a Darwin Core-Archive file. This will provide all data tables as separate files within a zipped folder * To mapper - this will open another browser with the data shown in the Mapper -![*Dataset download*](images/dataset-DL.png){width=70%} +![*Dataset download*](images/dataset-DL.png){width=90%} If you searched for aggregate datasets (e.g., all Crustacea records, all records from OBIS-Canada, etc.), the `source DwC-A` button will not be available to you. To download these data subsets, you must click `to mapper` and then [download the data from the Mapper as a CSV](#mapper). @@ -101,11 +101,11 @@ If you searched for aggregate datasets (e.g., all Crustacea records, all records To obtain a full export of OBIS data, navigate to the OBIS homepage, click on Data from the top navigation bar, then select [Data Access](https://obis.org/data/access/) from the dropdown menu. -![*OBIS homepage showing where to navigate to access full database exports*](images/full-export1.png){width=70%} +![*OBIS homepage showing where to navigate to access full database exports*](images/full-export1.png) Here you will be able to download all occurrence records as a CSV or Parquet file. Note the disclaimer that such exports will not include measurement data, dropped records, or absence records. As with downloads from the Mapper, the exported file is a single Occurrence table. This table includes all provided Event and Occurrence data, as well as 68 fields added by the OBIS Quality Control Pipeline, including taxonomic information obtained from WoRMS. -![*OBIS Data Access page*](images/full-export2.png){width=70%} +![*OBIS Data Access page*](images/full-export2.png) ## Finding your own data in OBIS diff --git a/common_formatissues.md b/common_formatissues.md index b951c71..2203ec1 100644 --- a/common_formatissues.md +++ b/common_formatissues.md @@ -4,7 +4,9 @@ - [Missing required fields](#missing-required-fields) - [Temporal issues: dates/times](#temporal-dates-and-times) -- [Spatial issues: coordinates, geographical formats](#spatial) +- [Historical data](#historical-data) +- [Spatial issues: coordinate conversion](#spatial) + - [Convert geographical formats](#geographical-format-conversion) ### Missing required fields @@ -105,7 +107,7 @@ For uncertainty regarding the date of the event, see [guidelines](common_qc.html To ensure your date is formatted correctly, it may be easiest to begin by populating the `year`, `month`, and `day` fields first. If the specific time of sampling is known, populate that into `eventTime` as well. When you fill these fields, we recommend ensuring the numbers are encoded as Text, not as General or numeric as Excel often tries to interpret what it thinks the content “should” be. Otherwise you may run into problems with Excel auto formatting your numbers in ways you don’t want. You can do this by highlighting the cells of interest, navigating to the Number Format on the Home ribbon and selecting “Text”. Be careful when you do this change of format, as some columns (e.g. time) may become formatted into a decimal or other unexpected format. -![Screenshot of how to change data type in Excel](images/excel-text-format.png){width=50%} +![*Screenshot of how to change data type in Excel*](images/excel-text-format.png){width=70%} Then you can use Excel to concatenate each field together, adding the time zone at the end, using the general format: @@ -113,7 +115,7 @@ Then you can use Excel to concatenate each field together, adding the time zone =CONCAT(YEAR, "-", MONTH, "-", DAY, "T", EVENTTIME, TIMEZONE) ``` -![Example of how to concatenate dates in Excel](images/excel-concatexample.png){width=40%} +![*Example of how to concatenate dates in Excel*](images/excel-concatexample.png){width=70%} > Note > You can also use the Canadensys [date parsing](https://data.canadensys.net/tools/dates) tool to help you convert dates or parse them into component parts. @@ -153,7 +155,7 @@ Our example dataset would then look like the following: You can see that the eventDate for the parent events does not need to be provided - only the dates for the actual samples are required. -#### Historical data +### Historical data Formatting historical data (data published before 1583 CE) can pose additional challenges due to restraints with the ISO 8601 standards. Namely, the shift from the Julian calendar to the currently used Gregorian calendar, as well as issues arising from the definition of [Year Zero](https://en.wikipedia.org/wiki/Year_zero). @@ -169,7 +171,7 @@ More specific guidelines to address historical data complications are under deve All coordinates provided in the `decimalLatitude` or `decimalLongitude` fields in OBIS must be in decimal degrees. To convert coordinates from degrees-minutes-seconds into decimal degrees, you can use [this Coordinate Conversion tool](https://obis.shinyapps.io/coordinates/) that OBIS has developed. This tool will convert any coordinate (or list of coordinates on a separate line) in a degrees-minutes-seconds format into decimal degrees, even partial coordinates. To use it, simply copy and paste your coordinates into the box provided and click Convert. For example: -![Screenshot of how to use the OBIS coordinate converter](images/coordinate_conversion.png){width=40%} +![*Screenshot of how to use the OBIS coordinate converter*](images/coordinate_conversion.png){width=70%} The [Map Tool tutorial](access.html#mapper) also reviews use of the coordinate conversion tool. @@ -183,23 +185,23 @@ In OBIS, the spatial reference system to be documented in `geodeticDatum` is [EP You can load a .csv file containing your coordinates to be reprojected into [QGIS](https://qgis.org/en/site/forusers/download.html). Opening a new project, first set the global projection to WGS84 EPSG:4326. In the bottom right corner, click the Project Properties to change the Project Coordinate Reference System (CRS). A pop up window will allow you to search for and select WGS84 EPSG:4326. Click OK. -![Screenshot of QGIS interface](images/qgis_screenshot1.png){width=60%} +![*Screenshot of QGIS interface*](images/qgis_screenshot1.png){width=70%} To load your .csv file containing the longitude and latitude coordinates, go to Layer < Add Layer < Add Delimited Text layer... -![How to add a .csv with coordinate data in QGIS](images/qgis_screenshot2.png){width=50%} +![*How to add a .csv with coordinate data in QGIS*](images/qgis_screenshot2.png){width=70%} A popup window will allow you to browse and select your .csv file. Open the `Geometry Definition` portion of the window and map the field containing longitude values to the `X field` and latitude to the `Y field`. Select the CRS that these coordinates were recorded as from the drop down menu. Then click `Add` and close the window. -![Screenshot showing how to specify CRS of a .csv file when importing into QGIS](images/qgis_screenshot3.png){width=50%} +![*Screenshot showing how to specify CRS of a .csv file when importing into QGIS*](images/qgis_screenshot3.png){width=70%} Go to Vector < Geometry Tools < Add Geometry Attributes -![Screenshot showing where to find the Geometry Attributes in QGIS menu](images/qgis_screenshot4.png){width=30%} +![*Screenshot showing where to find the Geometry Attributes in QGIS menu*](images/qgis_screenshot4.png){width=70%} Make sure the input layer is your coordinate file. Under the `Calculate using`, select Project CRS (because we set the Project CRS to the desired projection). Click `Run`. This will create a new layer with an additional two columns called Xcoord (longitude) and Ycoord (latitude). These fields contain the coordinates in the desired projection (i.e., WGS84). You can view these columns by right clicking and opening the layer’s attribute table. To export the file, right click the layer and click Make Permanent. Then save the .csv. -![Screenshot showing how to save a temporary layer in QGIS for export](images/qgis_screenshot5.png){width=40%} +![*Screenshot showing how to save a temporary layer in QGIS for export*](images/qgis_screenshot5.png){width=40%} For more details see this [QGIS guide on reprojection](https://docs.qgis.org/3.22/en/docs/training_manual/processing/crs.html?highlight=reproject). diff --git a/common_qc.md b/common_qc.md index 4eaa5e4..d5f83c7 100644 --- a/common_qc.md +++ b/common_qc.md @@ -57,11 +57,11 @@ 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`. -![Screenshot of Cook Strait page on the Getty Thersaurus](images/getty-thesaurus-NZexample.png){width=60%} +![*Screenshot of Cook Strait page on the Getty Thersaurus*](images/getty-thesaurus-NZexample.png){width=80%} For Google Maps, the coordinates can be found in the url after searching. -![Screenshot of Google Maps showing where coordinates can be foun din the URL](images/google-maps-coordinates.png){width=60%} +![*Screenshot of Google Maps showing where coordinates can be found in the URL*](images/google-maps-coordinates.png){width=80%} ### How to use Marine Regions Gazetteer tool @@ -69,16 +69,16 @@ Marine Regions offers a marine gazetteer search engine to obtain geographic info For this example we will search by geographic name for the Bay of Fundy. -![Marine regions gazetteer search](images/marinegazeeteer-search.png){width=50%} -![Marine regions gazetteer search](images/marinegazeeteer-bayfundy.png){width=60%} +![ ](images/marinegazeeteer-search.png){width=80%} +![*Marine regions gazetteer search*](images/marinegazeeteer-bayfundy.png){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: -![Bay of Fundy source IHO](images/marinegazeeteer-bayfundy-1-IHO.png){width=450%} -![Bay of Fundy source SeaVoX](images/marinegazeeteer-bayfundy-2-SeaVoX.png){width=50%} -![Canadian part of Bay of Fundy source Marine Region](images/marinegazeeteer-bayfundy-3-MarRegion.png){width=50%} -![Bay of Fundy source MEOW](images/marinegazeeteer-bayfundy-4-MEOW.png){width=50%} -![United States part of Bay of Fundy source Marine Region](images/marinegazeeteer-bayfundy-5-MarRegion.png){width=50%} +![*Bay of Fundy source IHO*](images/marinegazeeteer-bayfundy-1-IHO.png){width=50%} +![*Bay of Fundy source SeaVoX*](images/marinegazeeteer-bayfundy-2-SeaVoX.png){width=50%} +![*Canadian part of Bay of Fundy source Marine Region*](images/marinegazeeteer-bayfundy-3-MarRegion.png){width=50%} +![*Bay of Fundy source MEOW*](images/marinegazeeteer-bayfundy-4-MEOW.png){width=50%} +![*United States part of Bay of Fundy source Marine Region*](images/marinegazeeteer-bayfundy-5-MarRegion.png){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: @@ -86,7 +86,7 @@ Notice that no region has the exact same geographic extent. Let’s select the I 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 -![Screenshot of Marine Region placedetails, highlighting important information for OBIS](images/MarineRegions-Gazetteer_placedetails.png){width=40%} +![*Screenshot of Marine Region placedetails, highlighting important information for OBIS*](images/MarineRegions-Gazetteer_placedetails.png){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). -![Figure 1. Flow diagram with the main Open Nomenclature qualifiers associated with physical specimens. The degree of confidence in the correct identifier increases from the top down. More info and figure copied from [Open Nomenclature in the biodiversity era](https://doi.org/10.1111/2041-210X.12594).](images/fig1-openNomenclature.png){width=60%} +![*Figure 1. Flow diagram with the main Open Nomenclature qualifiers associated with physical specimens. The degree of confidence in the correct identifier increases from the top down. More info and figure copied from [Open Nomenclature in the biodiversity era](https://doi.org/10.1111/2041-210X.12594).*](images/fig1-openNomenclature.png){width=80%} -![Figure 2: Flow diagram with the main Open Nomenclature qualifiers for the identification of specimens from images (non-physical, image-based) . More information and figure copied from [Recommendations for the Standardisation of Open Taxonomic Nomenclature for Image-Based Identifications](https://www.frontiersin.org/articles/10.3389/fmars.2021.620702/full)](images/fig2-flowDiagram.jpg){width=60%} +![*Figure 2: Flow diagram with the main Open Nomenclature qualifiers for the identification of specimens from images (non-physical, image-based) . More information and figure copied from [Recommendations for the Standardisation of Open Taxonomic Nomenclature for Image-Based Identifications](https://www.frontiersin.org/articles/10.3389/fmars.2021.620702/full)*](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. -![Dropped records from a benthic macroalgae dataset](images/dropped-records1.png){width=40%} +![*Dropped records from a benthic macroalgae dataset*](images/dropped-records1.png){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. -![Flags specifying why certain records were dropped](images/dropped-records2.png){width=40%} +![*Flags specifying why certain records were dropped*](images/dropped-records2.png){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. -![ ](images/nonmarine-spp-worms.png){width=60%} +![ ](images/nonmarine-spp-worms.png){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. -![ ](images/nonmarine-spp-irmng.png){width=60%} +![ ](images/nonmarine-spp-irmng.png){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 info@marinespecies.org with your request along with your record or publication substantiating the addition/change. diff --git a/data_sharing.md b/data_sharing.md index 0ecec4b..cf54423 100644 --- a/data_sharing.md +++ b/data_sharing.md @@ -1,5 +1,12 @@ ## Maintaining and sharing published data +**Content** + +* [Add a DOI](#adding-a-doi-to-datasets) +* [User tracking](#user-tracking) +* [Update your own data](#update-your-data-in-obis) +* [Publish to OBIS and GBIF](#simultaneous-publishing-to-gbif) + ### Adding a DOI to datasets DOIs are important for tracking your dataset. Fortunately you can easily reserve a DOI for your dataset if the IPT administrator has configured the IPT accordingly. @@ -8,13 +15,13 @@ As the IPT administrator, you must enable the capacity for users to reserve DOIs Once this has been configured, a data provider or admin can easily reserve a DOI for a dataset. First log in to the IPT, navigate to the Manage Resources tab, then select the dataset for which you wish to reserve a DOI. On the overview page for the dataset, scroll to the Publication section, click the three vertical dots and select “Reserve DOI”. -![Screenshot indicating how to reserve a DOI for your dataset](images/ipt-doi.png){width=60%} +![*Screenshot indicating how to reserve a DOI for your dataset*](images/ipt-doi.png){width=80%} ### User tracking OBIS tracks the number of times your dataset is downloaded. This information is available on your dataset’s page under the Statistics box. -![Example screenshot of how dataset downloads can be tracked](images/data-tracking.png){width=60%} +![*Example screenshot of how dataset downloads can be tracked*](images/data-tracking.png){width=70%} ## Update your data in OBIS @@ -27,7 +34,7 @@ To update your own data in OBIS, the process is largely the same as [publishing The new version will be automatically updated. A new DOI will be generated only if you generate it yourself on the new version. Deciding when to generate a new DOI is up to you, but generally you should generate a new DOI when there have been major changes to your dataset, such as significant changes in your metadata or a move to a 2.0 resource version within the IPT. -![Example of IPT version control](images/ipt-pubVersion.png){width=60%} +![*Example of IPT version control*](images/ipt-pubVersion.png){width=80%} ## Simultaneous publishing to GBIF diff --git a/dna_data.md b/dna_data.md index 88b6b98..6725ffb 100644 --- a/dna_data.md +++ b/dna_data.md @@ -2,9 +2,9 @@ **Contents:** -- [Introduction](dna_data.html#introduction) -- [eDNA & DNA Derived use cases](dna_data.html#edna--dna-derived-data-example) -- [How to find genetic data in OBIS](dna_data.html#how-to-find-genetic-data-in-obis) +- [Introduction](#introduction) +- [eDNA & DNA Derived use cases](#edna-and-dna-derived-data-example) +- [How to find genetic data in OBIS](#how-to-find-genetic-data-in-obis) #### Introduction @@ -76,7 +76,7 @@ OBIS is developing guidelines and pipelines to accept other data types, such as: - [Tracking](other_data_types.html#tracking-data) - [Habitat](other_data_types.html#habitat-data) -#### eDNA & DNA derived data example +#### eDNA and DNA derived data example The following example use cases draw on both the [GBIF guide](https://docs.gbif-uat.org/publishing-dna-derived-data/1.0/en/) and the [DNA derived data extension](https://rs.gbif-uat.org/extensions.html#http) to illustrate how to incorporate a DNA derived data extension file into a Darwin Core archive. Note: for the purposes of this section, only required Occurrence core terms are shown, in addition to all eDNA & DNA specific terms. For additional Occurrence core terms, refer to [Occurrence](darwin_core.html#occurrence). diff --git a/ipt.md b/ipt.md index 5dec168..91a4fa6 100644 --- a/ipt.md +++ b/ipt.md @@ -20,13 +20,13 @@ Before we get into the details for accessing and using the IPT, let’s understa All these components (i.e., core file, extension files, descriptor file, and metadata file) become compressed together (as a .zip file) and comprise the Darwin Core Archive. -![Example showing how Occurrence core, EML, and meta.xml files make up a Darwin Core-Archive file](images/dwca_1.png){width=70%} +![*Example showing how Occurrence core, EML, and meta.xml files make up a Darwin Core-Archive file*](images/dwca_1.png){width=70%} ### How to access the IPT Once you have determined which [OBIS node IPT](https://ipt.iobis.org/) is suited for your dataset, you can contact your node manager to create an associated account for you. There will be a link on the sign in page that will direct you to the IPT’s administrator to contact them. If your node’s IPT is not listed here, you will have to [contact the node manager](https://obis.org/contact/) to get the link to their IPT. -![Screenshot of IPT login page, highlighting link to IPT admin and the login button](images/ipt-login.png){width=70%} +![*Screenshot of IPT login page, highlighting link to IPT admin and the login button*](images/ipt-login.png){width=90%} If you are an IPT admin and want to know how to set up an IPT yourself, see the [IPT admin page](ipt_admin.html). @@ -48,7 +48,7 @@ Desmet, P. & C. Sinou. 2012. 7-step guide to data publication. Canadensys. Metadata and click Edit to open the metadata editor. Any information you provide here will be visible on the resource homepage and bundled together with your data when you publish. -![Screenshot showing where to add or upload metadata](images/ipt-ss12-metadata.png){width=70%} +![*Screenshot showing where to add or upload metadata*](images/ipt-ss12-metadata.png){width=80%} 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. @@ -154,17 +154,17 @@ Follow the guidelines on the [OBIS metadata standards and best practices](eml.ht With your dataset uploaded, properly mapped to DwC, and all the metadata filled, you can publish your dataset. On your resource overview page, go to the Publication section, click the vertical dots and select Publish. -![Screenshot showing where to manage the publishing of your dataset](images/ipt-ss7-pub.png){width=70%} +![*Screenshot showing where to manage the publishing of your dataset*](images/ipt-ss7-pub.png){width=80%} The IPT will now generate your data as Darwin Core, and combine the data with the metadata to package it as a standardized zip-file called a “Darwin Core Archive”. See the IPT manual for more details. > **Note:** Hitting the "publish" button does not mean that your dataset is available to everyone, it is still private, with access limited to the resource managers. It will only be publicly available when you have changed Visibility to Public. You can choose to do this immediately or at a set date. -![Screenshot showing how to change the visibility of your dataset](images/ipt-ss9-vis.png){width=70%} +![*Screenshot showing how to change the visibility of your dataset*](images/ipt-ss9-vis.png){width=80%} Your dataset will only be harvested by GBIF when you change Registration to Registered. This step is not needed for OBIS to harvest your datasets. Please do not register your dataset with GBIF if your dataset is already published in GBIF by another publisher. Note that the IPT itself must be [registered with GBIF](ipt_admin.html) in order to publish to GBIF. The node manager can do this. -![Screenshot showing where to register your dataset with GBIF. This is only available if the IPT itself is registered with GBIF as well.](images/ipt-ss8-gbifreg.png){width=70%} +![*Screenshot showing where to register your dataset with GBIF. This is only available if the IPT itself is registered with GBIF as well.*](images/ipt-ss8-gbifreg.png){width=70%} Back on the resource overview page > Published Release, you can see the details of your first published dataset, including the publication date and the version number. Since your dataset is published privately, the only thing left to do is to click Visibility to Public (see the IPT manual) to make it available to everyone. @@ -184,8 +184,8 @@ The Metadata expressed in the EML Profile standard can also be downloaded as a R To download a dataset from an IPT, simply login, and from the home page (not the Manage Resources tab) search for the dataset in question. You can search for keywords in the Filter box on the right side of the page. -![Overview of home page of an IPT](images/ipt-ss10-download1.png){width=70%} +![*Overview of home page of an IPT*](images/ipt-ss10-download1.png){width=90%} Once you navigate to the page of a dataset, at the top of the page you will have options to download the whole Darwin Core Archive file, or just the metadata as an EML or RTF file. -![Overview of a dataset page on an IPT, emphasizing where to download the resource](images/ipt-ss11-download2.png){width=70%} +![*Overview of a dataset page on an IPT, emphasizing where to download the resource*](images/ipt-ss11-download2.png){width=90%} diff --git a/ipt_admin.md b/ipt_admin.md index 36f24c9..5fb3273 100644 --- a/ipt_admin.md +++ b/ipt_admin.md @@ -32,10 +32,10 @@ As the IPT administrator, you must make sure the IPT is kept up to date, dataset To add or update extensions, navigate to the Darwin Core Types and Extensions page from the Administration menu. To install an extension (e.g., DNA Derived Data), simply scroll down the page and click the `Install` button to the right of the desired extension. -![Screenshot of IPT Admin page](images/iptadmin-installex.png){width=70%} +![*Screenshot of IPT Admin page*](images/iptadmin-installex.png) For extensions already installed, you may notice yellow flags indicating a core or extension is out of date. You can update these easily by clicking the `Update` button. -![Screenshot demonstrating when core or extensions need to be updated](images/iptadmin-core.png){width=70%} +![*Screenshot demonstrating when core or extensions need to be updated*](images/iptadmin-core.png) For a detailed breakdown of administrator options, see the [IPT guide](https://github.com/gbif/ipt/wiki/IPT2ManualAdministration.wiki#administration-menu). diff --git a/lifewatch_qc.md b/lifewatch_qc.md index 3a7ffb8..9452f9a 100644 --- a/lifewatch_qc.md +++ b/lifewatch_qc.md @@ -1,4 +1,4 @@ -### Geographic and data format quality control +## Geographic and data format quality control These Data validation and QC services are available on the LifeWatch portal at [http://www.lifewatch.be/data-services](http://www.lifewatch.be/data-services). diff --git a/mofreports.md b/mofreports.md index 5b55cfd..2d1b7a1 100644 --- a/mofreports.md +++ b/mofreports.md @@ -16,7 +16,7 @@ Example, selected OBIS USA, then selected Florida Keys Reef Visual Census 1994, and scrolled down to MEASUREMENT TYPES section: - +![ ](images/mofreports/floridakeys.png) To locate other datasets using these MEASUREMENT TYPES, use this active filtering MoF tool , sort by measurementType (click column header) and scroll to measurementType(s) of interest @@ -32,7 +32,7 @@ For MEASUREMENT TYPE “fish length” … To see which datasets are using this There are two records for fish length, one missing an ID and the other using S06, which may not be the preferred ID for this measurementType: - +![ ](images/mofreports/fishlength.png) Also, while scrolling through this report, you may notice something you would like to further research, click the record count value to see a list of datasets and associated node(s) using this noted type/ID. NOTE: Current USE does not indicate CORRECT use: diff --git a/other_data_types.md b/other_data_types.md index 39ea5ba..14c830d 100644 --- a/other_data_types.md +++ b/other_data_types.md @@ -1,3 +1,9 @@ +**Content** + +- [Multimedia data](#multimedia-data-acoustic-imaging) +- [Habitat data](#habitat-data) +- [Tracking data](#tracking-data) + ### Multimedia data (Acoustic, Imaging) If you have multimedia data (e.g. images, acoustic, video) that you want to publish alongside your dataset, you can do so by documenting information in the `associatedMedia` field in your Occurrence table. The usage of this field requires the media in question to be hosted somewhere, e.g., a publication, museum database, etc. Then you simply copy this link to the `associatedMedia` field for a given occurrence. You may also include a concatenated list if you need to list multiple sources.