diff --git a/jupyterbook/_toc.yml b/jupyterbook/_toc.yml index 95565425..462e4128 100644 --- a/jupyterbook/_toc.yml +++ b/jupyterbook/_toc.yml @@ -2,6 +2,11 @@ format: jb-book root: content/intro.md title: The IOOS Data Demo Center parts: + - caption: Getting Started + chapters: + - file: content/ioos_installation_conda.md + title: Installing the IOOS Conda Environment + - caption: Code Gallery chapters: - file: content/code_gallery/data_access.md @@ -22,8 +27,6 @@ parts: - caption: Other Resources chapters: - - file: content/ioos_installation_conda.md - title: Installing the IOOS Conda Environment - url: https://help.aodn.org.au/aodn-data-tools/user-code-library/ title: Opening netCDF files - hints from AODN - url: http://unidata.github.io/notebook-gallery/ diff --git a/jupyterbook/content/code_gallery/data_access.md b/jupyterbook/content/code_gallery/data_access.md index 7f6dbd97..117ff260 100644 --- a/jupyterbook/content/code_gallery/data_access.md +++ b/jupyterbook/content/code_gallery/data_access.md @@ -1,3 +1,23 @@ # Data Access -This chapter will consist of all the notebooks pertaining to data access +IOOS data comes from a variety of technologies or data collection systems. While types of data available through any +one of our 11 regional associations may vary depending on the local area, the national IOOS data products include data +collected from buoys, high frequency radar systems and gliders. Modeling teams across regional associations also create +data products including physical and environmental models of coastal systems. + +IOOS data can be accessed through a variety of access services and tools through IOOS interactive maps, Data Assembly +Centers (DACs), and individual Regional Association portals. This chapter provides examples of the various data access +services (SOS, THREDDS, ERDDAP, etc) and tools for scientists and managers looking to access data using various programing languages (Python, +Matlab, R, etc). + +For more information on accessing IOOS data, see . + +--- + +## Chapter table of contents + +```{tableofcontents} + +``` + +--- diff --git a/jupyterbook/content/code_gallery/data_analysis_and_visualization.md b/jupyterbook/content/code_gallery/data_analysis_and_visualization.md index fd0a6c46..8b45b09c 100644 --- a/jupyterbook/content/code_gallery/data_analysis_and_visualization.md +++ b/jupyterbook/content/code_gallery/data_analysis_and_visualization.md @@ -1,3 +1,13 @@ # Data Analysis And Visualization This chapter will consist of notebooks pertaining to data analysis. + +--- + +## Chapter table of contents + +```{tableofcontents} + +``` + +--- diff --git a/jupyterbook/content/code_gallery/data_management.md b/jupyterbook/content/code_gallery/data_management.md index 54982f2a..d1127d08 100644 --- a/jupyterbook/content/code_gallery/data_management.md +++ b/jupyterbook/content/code_gallery/data_management.md @@ -1,3 +1,15 @@ # Data Management -This chapter will contain all the notebooks pertaining to Data Management +Data management is an increasingly important aspect of IOOS activities. In this chapter you will find examples of how +to use various tools to ensure compliance with existing standards and conventions. For more details on IOOS +recommendations on data standards, see . + +--- + +## Chapter table of contents + +```{tableofcontents} + +``` + +--- diff --git a/jupyterbook/content/code_gallery/data_management_notebooks/2020-12-08-DataToDwC.ipynb b/jupyterbook/content/code_gallery/data_management_notebooks/2020-12-08-DataToDwC.ipynb index cadff0ed..ccb76f40 100644 --- a/jupyterbook/content/code_gallery/data_management_notebooks/2020-12-08-DataToDwC.ipynb +++ b/jupyterbook/content/code_gallery/data_management_notebooks/2020-12-08-DataToDwC.ipynb @@ -260,7 +260,7 @@ "id": "HRAnbhZgW4Qk" }, "source": [ - "# Event file" + "## Event file" ] }, { @@ -546,7 +546,7 @@ "id": "-aHsrOUhW4Qo" }, "source": [ - "# Occurrence file\n", + "## Occurrence file\n", "More information on the **occurrence** category in Darwin Core can be found at [https://dwc.tdwg.org/terms/#occurrence](https://dwc.tdwg.org/terms/#occurrence).\n", "\n", "For creating the **occurrence** file, we start by creating the DataFrame and renaming the fields that align directly with Darwin Core. Then, we'll add the required information that is missing." @@ -571,7 +571,7 @@ "id": "CzjlzVcYW4Qo" }, "source": [ - "## Taxonomic Name Matching\n", + "### Taxonomic Name Matching\n", "A requirement for [OBIS](https://obis.org/) is that all scientific names match to the [World Register of\n", "Marine Species (WoRMS)](http://www.marinespecies.org/) and a `scientificNameID` is included. A `scientificNameID` looks\n", "like this `urn:lsid:marinespecies.org:taxname:275730` with the last digits after\n", @@ -1159,7 +1159,7 @@ "id": "dUufvx_uW4Qr" }, "source": [ - "# Extended Measurement Or Fact (eMoF)\n", + "## Extended Measurement Or Fact (eMoF)\n", "The last file we need to create is the **extended measurement or fact (eMoF)** file. The measurement or fact includes measurements/facts about the event (temp, salinity, etc) as well as about the occurrence (percent cover, abundance, weight, length, etc). They are linked to the events using `eventID` and to the occurrences using `occurrenceID`. [Extended Measurements Or Facts](https://tools.gbif.org/dwca-validator/extension.do?id=http://rs.iobis.org/obis/terms/ExtendedMeasurementOrFact) are any other generic observations that are associated with resources that are described using Darwin Core (eg. water temperature observations). See the [DwC implementation guide](https://dwc.tdwg.org/rdf/#2-implementation-guide) for more information.\n", "\n", "For the various `TypeID` fields (eg. `measurementTypeID`) include URI's from the [BODC NERC vocabulary](https://www.bodc.ac.uk/resources/vocabularies/vocabulary_search/) or other *nearly permanent* source, where possible. For example, [water temperature](http://vocab.nerc.ac.uk/collection/P25/current/WTEMP/) in the BODC NERC vocabulary, the URI is `http://vocab.nerc.ac.uk/collection/P25/current/WTEMP/`.\n", @@ -1501,7 +1501,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.6" + "version": "3.9.10" } }, "nbformat": 4,