Merge branch 'main' of github.com:sformel-usgs/bds-primer-best-practices

CONTEXT_UNDERSTANDABILITY.qmd

@@ -17,7 +17,7 @@ Ecological Metadata Language (EML) is an XML schema. An EML instance (XML docume
 
 ### Key Information
 
--   EML schema <https://eml.ecoinformatics.org/eml-schema> 
+-   [EML Schema](https://eml.ecoinformatics.org/eml-schema)
 
 -   Mandatory for LTER, iLTER, OBIS, GBIF, Darwin Core Archive (DwC-A)
 
@@ -31,17 +31,17 @@ Tools or packages to help write EML:
 
 -   For data managers, coders: 
 
-    -   EML-R package: <https://cran.r-project.org/web/packages/EML/index.html>
+    -   [EML-R package](https://cran.r-project.org/web/packages/EML/index.html)
 
-    -   Postgresql database with fields compatible with EML <https://github.com/lter/LTER-core-metabase>  
+    -   [Postgresql database with fields compatible with EML](https://github.com/lter/LTER-core-metabase)
 
-    -   R-code for generating EML from LTER-metabase (built on EML-R package): <https://github.com/BLE-LTER/MetaEgress>
+    -   [R-code for generating EML from LTER-metabase (built on EML-R package)](https://github.com/BLE-LTER/MetaEgress)
 
-    -   EMLAssemblyline (built on EML-R package): <https://ediorg.github.io/EMLassemblyline/articles/overview.html> 
+    -   [EMLAssemblyline (built on EML-R package)](https://ediorg.github.io/EMLassemblyline/articles/overview.html)
 
 -   For scientists or those not inclined to write scripts
 
-    -   ezEML: <https://ezeml.edirepository.org/>
+    -   [ezEML](https://ezeml.edirepository.org/)
 
 ## ISO 19115
 
@@ -69,24 +69,21 @@ Content standard for describing geographic data sponsored by the International S
 
     -   ISO 19115 Geographic information -- Metadata: The ISO standard for documenting geospatial data. 
 
-    -   ISO 19115-2 Geographic information -- Metadata -- Part 2: Extensions for imagery and gridded data: An extension of ISO 19115 used to document information about imagery, gridded data, and remotely sensed data. The root of ISO 19115 metadata records will change from MD_Metadata to MI_Metadata when using ISO 19115-2. 
-
--   There is a biological extension (https://repository.oceanbestpractices.org/handle/11329/1281?show=full), but it is not very widely used.  In part this is because many search engines do not harvest this extension.
+    -   ISO 19115-2 Geographic information -- Metadata -- Part 2: Extensions for imagery and gridded data: An extension of ISO 19115 used to document information about imagery, gridded data, and remotely sensed data. The root of ISO 19115 metadata records will change from MD_Metadata to MI_Metadata when using ISO 19115-2.
 
 -   Usurped FGDC CSDGM - all users encouraged to migrate to ISO.
 
 -   Highly flexible for many uses compared FGDC CSDGM, but few required elements leaves room for incomplete metadata
 
 ### Top References
 
--   NOAA Workbook for ISO 19115-2 <https://www.ncei.noaa.gov/sites/default/files/2020-04/ISO%2019115-2%20Workbook_Part%20II%20Extentions%20for%20imagery%20and%20Gridded%20Data.pdf> 
+-   [NOAA Workbook for ISO 19115-2](https://www.ncei.noaa.gov/sites/default/files/2020-04/ISO%2019115-2%20Workbook_Part%20II%20Extentions%20for%20imagery%20and%20Gridded%20Data.pdf) 
 
--   Convert ISO to EML - <https://nceas.github.io/arcticdatautils/reference/convert_iso_to_eml.html> 
+-   [How to Convert ISO to EML](https://nceas.github.io/arcticdatautils/reference/convert_iso_to_eml.html) 
 
--   Work Flow Model -\
-    <https://www.fgdc.gov/metadata/iso-implementation-model-workflow> 
+-   [Work Flow Model](https://www.fgdc.gov/metadata/iso-implementation-model-workflow)
 
--   mdToolkit: <https://www.mdtoolkit.org/home> - mdEditor is a writer for ISO 19115 metadata which uses mdJSON as an intermediary and mdTranslator allows translation to different metadata formats
+-   [mdToolkit](https://www.mdtoolkit.org/home) - mdEditor is a writer for ISO 19115 metadata which uses mdJSON as an intermediary and mdTranslator allows translation to different metadata formats
 
 ## Minimum Information about any (x) Sequence (MIxS)
 
@@ -104,24 +101,20 @@ A set of checklists and packages for genomic sequence data
 
 ### Key Information
 
--   Pronounced "mix-ess"
-
--   Term search tool: <http://www.gensc.org/pages/standards/search-terms.html>?
+-   MIxS (pronounced MIX-ess) is a suite of checklists standards introduced the reporting of a breadth of environment-specific metadata variables to augment the genome-specific checklists.
 
--   MixS is a suite of checklists (pronounced MIX-ess) standards introduced the reporting of a breadth of environment-specific metadata variables to augment the genome-specific checklists.
+-   Enables mixing and matching of genome checklists and environmental-specific packages.
 
--   Thus enabling the mix and matching of genome checklists and environmental-specific packages.
-
--   [![MixS Structure](http://www.gensc.org/images/mixs_ext_graphic-1024x731.png)](http://www.gensc.org/pages/standards-intro.html)
+-   [![MIxS Structure](http://www.gensc.org/images/mixs_ext_graphic-1024x731.png)](http://www.gensc.org/pages/standards-intro.html)
 
 ### Top References
+
+-   [MIxS Term Search Tool](http://www.gensc.org/pages/standards/search-terms.html)
 
--   <https://genomicsstandardsconsortium.github.io/mixs/>
-
--   <https://www.gensc.org/mixs/> 
+-   [Genomic Standards Consortium term list](https://genomicsstandardsconsortium.github.io/mixs/)
 
--   <https://www.nature.com/articles/nbt.1823>
+-   [Minimum Information about Marker Gene Sequence (MIMARKS)](https://www.nature.com/articles/nbt.1823)
 
--   <https://github.com/GenomicsStandardsConsortium/mixs/wiki> 
+-   [MIxS GitHub repo](https://github.com/GenomicsStandardsConsortium/mixs)
 
--   <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3869023/>
+-   [Minimum Information about Sequence Data from the Built Environment (MIxS-BE)](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3869023/)

README.md

@@ -1,8 +1,8 @@
 # ESIP BDS Primer Best Practice Suite of Documents
-The [ESIP Biological Data Standards Cluster](https://wiki.esipfed.org/Biological_Data_Standards_Cluster) formed in 2020 to maximize data relevance and utility for understanding changes in biodiversity over time. To accomplish this the cluster facilitates guidance, best practice documentation, training, and community building for the US biological data community. The first product from this cluster [Biological Data Standards Primer](https://doi.org/10.6084/m9.figshare.16806712.v2), while an easy to digest resource, does not provide the context data managers need to decide which standards to use for the data they are working with. The best practice documents are intended to be a bridge between the full, lengthy standards documentation, and the short primer quick reference.
+The [ESIP Biological Data Standards Cluster](https://wiki.esipfed.org/Biological_Data_Standards_Cluster) formed in 2020 to maximize data relevance and utility for understanding changes in biodiversity over time. To accomplish this the cluster facilitates guidance, documentation, training, and community building for the US biological data community. The first product from this cluster [Biological Data Standards Primer](https://doi.org/10.6084/m9.figshare.16806712.v2), while an easy to digest resource, does not provide the context data managers need to decide which standards to use for the data they are working with. The guideline documents [this repo] are intended to be a bridge between the full, lengthy standards documentation, and the short primer quick reference.
 
 ## Why
-While the primer provided a quick reference it didn't provide enough context for new data managers to make decisions on which standards would be best to implement for the data they are working with. This suite of best practice documents is intended to provide a bit more information than what you see in the primer but not the full standards documentation. The suite of documents will pair with the different sections of the primer. The first document being developed is for the "Make Your Data Software Ready?" section of the primer.
+While the primer provided a quick reference it didn't provide enough context for new data managers to make decisions on which standards would be best to implement for the data they are working with. This suite of guidelines documents is intended to provide a bit more information than what you see in the primer but not the full standards documentation. The suite of documents will pair with the different sections of the primer. The first document being developed is for the "Make Your Data Software Ready?" section of the primer.
 
 ## How to contribute
-If you would like to suggest changes or additions to the current version of the best practice documents, please use the [GitHub issues](https://github.com/ESIPFed/bds-primer-best-practices/issues/new/choose) to document your request. The current draft can be seen as a rendered webpage [here](https://esipfed.github.io/bds-primer-best-practices/introduction.html).
+If you would like to suggest changes or additions to the current version of the guideline documents, please use the [GitHub issues](https://github.com/ESIPFed/bds-primer-best-practices/issues/new/choose) to document your request. The current draft can be seen as a rendered webpage [here](https://esipfed.github.io/bds-primer-best-practices/).