fix: v1.1.1 refactor

dylanporyan · web-flow · commit 3efbaaf4d9e6 · 2025-03-28T16:57:21.000-07:00
- SUMMARY.md
- contribute.md
- instructions.md
- README.md
- guide.md
diff --git a/README.md b/README.md
@@ -1,8 +1,8 @@
-# ESS-DIVE Sample ID and Metadata Reporting Format (IGSN-ESS) v1.1.0
+# ESS-DIVE Sample ID and Metadata Reporting Format v1.1.1
 
 ESS-DIVE recommends registering samples for [Global Sample Numbers (IGSNs)](https://www.igsn.org/) through the [System for Earth Sample Registration (SESAR)](https://www.geosamples.org/). IGSNs are associated with standardized metadata to characterize a variety of different samples and their collection details. These sample identifiers facilitate sample discovery, tracking, and reuse; they are especially useful when sample data is shared with collaborators, sent to different labs or user facilities for analyses, or distributed in different data files, datasets, and/or publications. 
 
-ESS-DIVE has worked with our community scientists to test use of IGSNs and associated metadata in interdisciplinary Environmental Systems Science (ESS). Here we outline modified IGSN metadata guidelines to account for needs of a variety of related geological and biological samples. While generally following the IGSN core descriptive metadata schema, we provide recommendations for extending sample type terms, and connecting to related templates geared towards biodiversity (Darwin Core) and genomic (Minimum Information about any Sequence, MIxS) samples and specimens. The resulting template and recommendations are an extension of IGSN core metadata - IGSN for Environmental Systems Science (IGSN-ESS). 
+ESS-DIVE has worked with our DOE ESS scientists to test use of IGSNs and associated metadata in interdisciplinary Environmental Systems Science (ESS). Here we outline modified IGSN metadata guidelines to account for needs of a variety of related geological and biological samples. While generally following the IGSN core descriptive metadata schema, we provide recommendations for extending sample type terms, and connecting to related templates geared towards biodiversity (Darwin Core) and genomic (Minimum Information about any Sequence, MIxS) samples and specimens. The resulting template and recommendations are an extension of IGSN core metadata - IGSN for Environmental Systems Science (IGSN-ESS). 
 
 ## Getting started
 
@@ -12,8 +12,8 @@ Other documents to get started:
 - [Instructions document](instructions.md): Instructions to register samples for IGSNs through SESAR, and submit related datasets to ESS-DIVE. 
 - [Sample metadata template](sampleTemplate.xls): Download spreadsheet template with standard fields to register samples for IGSNs. 
 
-## Updates in v1.1.0  
-- This is the second release of the Sample ID and Metadata Reporting Format  
+## Updates in v1.1.1 
+In March 2025, a patch version of the Sample ID and Metadata reporting format was made to improve the overall experience with the associated reporting format documentation. Additionally, the standard reporting format keyword and standard term were added to the instructions.md file.
 
 ## File formatting requirements
 
@@ -27,7 +27,7 @@ ESS-DIVE has higher-level requirements and recommendations for documenting indiv
 
 ## How to contribute: 
 
-Want to make a change to the reporting format? [Submit a new issue](https://github.com/ess-dive-community/essdive-sample-id-metadata/issues/new/choose) and use one of several templates that we provide to: suggest a new term, modify a term, or propose changes to documentation within this repository.
+Want to make a change to the reporting format? [Submit a new issue](https://github.com/ess-dive-workspace/essdive-sample-id-metadata/issues/new/choose) and use one of several templates that we provide to: suggest a new term, modify a term, or propose changes to documentation within this repository.
 
 Have a question? Contact us at ess-dive-support [at] lbl.gov. 
 
@@ -59,11 +59,11 @@ The ESS-DIVE Sample ID and metadata reporting format (IGSN-ESS) is licensed unde
 
 Funding for the development of ESS-DIVE's Sample ID and metadata reporting format was provided by the US Deparment of Energy (DOE), Biological and Environmental Research Program, Earth and Environmental Systems Sciences Division, Data Management.
 
-The updated sample reporting format for interdisciplinary ESS samples contains modifications and extensions of guidelines originally created by the System for Earth Sample Registration (SESAR) and IGSN organization. Individuals within these organizations are responsible for creating IGSN identifiers and standard sample metadata templates. We especially thank Kerstin Lehnert, Jens Klump, Lesley Wyborn, and Sarah Ramdeen for their development and engagement work, and/or direct assistence with using IGSN. 
+The updated sample reporting format for interdisciplinary ESS samples contains modifications and extensions of guidelines originally created by the System for Earth Sample Registration (SESAR) and IGSN organization. Individuals within these organizations are responsible for creating IGSN identifiers and standard sample metadata templates. We especially thank Kerstin Lehnert, Jens Klump, Lesley Wyborn, and Sarah Ramdeen for their development and/or direct assistance with using IGSN. 
 
 As outlined in the [sample metadata sources](/terms/sampleMetadata_sources.md) document, many recommended metadata additions to the IGSN guidelines/schema come from Darwin Core, and MIxS. We utilize formats for our user guides from [Darwin Core resources](https://github.com/tdwg/dwc), as well.  
 
-ESS community scientists helped test use of IGSNs, and provided critical feedback - resulting in our final recommendations. These include individuals from eight ESS projects, including: 
+ESS scientists helped test use of IGSNs, and provided critical feedback - resulting in our final recommendations. These include individuals from eight ESS projects, including: 
 - SLAC Subsurface Biogeochemical Research (SBR) Scientific Focus Area (SFA), National Accellerator Laboratory Groundwater Quality: Zach Perzan and Kristin Boye
 - Lawrence Livermore National Lab SBR SFA, Subsurface Biogeochemistry of Actinides: Nancy Merino and Mavrik Zavarin
 - Pacific Northwest National Lab SBR SFA, Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS): Amy Goldman and James Stegen
diff --git a/SUMMARY.md b/SUMMARY.md
@@ -5,12 +5,12 @@
 * [Guide](guide.md)
 * [Term lists](term-lists/README.md)
   * [materials](terms/material.md)
-  * [material translation table](https://github.com/ess-dive-community/essdive-sample-id-metadata/blob/master/terms/material_translation_table.csv)
+  * [material translation table](terms/material_translation_table.csv)
   * [object type](terms/objectType.md)
-  * [object type translation table](https://github.com/ess-dive-community/essdive-sample-id-metadata/blob/master/terms/objectType_translation_table.csv)
-  * [sample metadata translation table](https://github.com/ess-dive-community/essdive-sample-id-metadata/blob/master/terms/sampleMetadataTranslationTable.csv)
+  * [object type translation table](terms/objectType_translation_table.csv)
+  * [sample metadata translation table](terms/sampleMetadataTranslationTable.csv)
   * [sample metadata sources](terms/sampleMetadata_sources.md)
   * [units](terms/units.md)
-* [Template](https://github.com/ess-dive-community/essdive-sample-id-metadata/blob/master/terms/sampleMetadataTranslationTable.xlsx)
+* [Template](sampleTemplate.xls)
 * [Contribute](contribute.md)
 * [License](LICENSE.md)
diff --git a/contribute.md b/contribute.md
@@ -2,7 +2,7 @@
 
 Here's how you can contribute to ESS-DIVE's proposed sample ID and metadata reporting format:
 
-* Want to make a change to the reporting format? Copy and paste one of the **issue templates** below and [submit a new issue](https://github.com/ess-dive-community/essdive-sample-id-metadata/issues/new).
+* Want to make a change to the reporting format? Copy and paste one of the **issue templates** below and [submit a new issue](https://github.com/ess-dive-workspace/essdive-sample-id-metadata/issues/new).
 * Have a question? Contact us at ess-dive-support@lbl.gov. 
 
 ---
@@ -16,7 +16,7 @@ Darwin Core maintenance group, Biodiversity Information Standards (TDWG) (2014).
 
 ### New term
 
-Copy and paste this template into your [new issue](https://github.com/ess-dive-community/essdive-sample-id-metadata/issues/new) if you want to create a term that does not exist yet.
+Copy and paste this template into your [new issue](https://github.com/ess-dive-workspace/essdive-sample-id-metadata/issues/new) if you want to create a term that does not exist yet.
 
 ```
 ## New term
@@ -37,7 +37,7 @@ Proposed definition of the new term:
 
 ### Change term
 
-Copy and paste this template into your [new issue](https://github.com/ess-dive-community/essdive-sample-id-metadata/issues/new) if you want to make a change to a term.
+Copy and paste this template into your [new issue](https://github.com/ess-dive-workspace/essdive-sample-id-metadata/issues/new) if you want to make a change to a term.
 
 ```
 ## Change term
@@ -60,7 +60,7 @@ I suggest the following changes (leave blank whatever would not change):
 
 ### Change documentation
 
-Copy and paste this template into your [new issue](https://github.com/ess-dive-community/essdive-sample-id-metadata/issues/new) if you want to make a change to the documentation.
+Copy and paste this template into your [new issue](https://github.com/ess-dive-workspace/essdive-sample-id-metadata/issues/new) if you want to make a change to the documentation.
 
 ```
 ## Change documentation
diff --git a/guide.md b/guide.md
@@ -1,8 +1,8 @@
 # ESS-DIVE Sample ID and Metadata Guide
 
-Here you will find proposed guidelines for standardizing sample metadata to describe interdisciplinary samples within DOE's Environmental Systems Science community.
+Here you will find proposed guidelines for standardizing sample metadata to describe interdisciplinary samples within DOE's Environmental Systems Science research.
 
-Most of the sample metadata follows [SESAR's metadata guidelines](http://doi.org/10.5281/zenodo.3874923). However, we modified some metadata elements, specific requirements, and vocabularies based on ESS community needs. This includes additional fields, which mostly come from biodiversity standards [Darwin Core](https://dwc.tdwg.org/), or genomic standards [Minimum Information about any Sequence (MIxS)](https://gensc.org/mixs/). 
+Most of the sample metadata follows [SESAR's metadata guidelines](http://doi.org/10.5281/zenodo.3874923). However, we modified some metadata elements, specific requirements, and vocabularies based on ESS researcher needs. This includes additional fields, which mostly come from biodiversity standards [Darwin Core](https://dwc.tdwg.org/), or genomic standards [Minimum Information about any Sequence (MIxS)](https://gensc.org/mixs/). 
 
 We seek any additional feedback, with the goal of making ESS sample information **F**indable, **A**ccessible, **I**nteroperable, and **R**eusable (FAIR). 
 
diff --git a/instructions.md b/instructions.md
@@ -23,7 +23,7 @@ When sending a sample to multiple labs for a variety of analyses that need to be
 
 ## Standardize Sample Metadata
 
-Complete the [sample template](https://github.com/ess-dive-community/essdive-sample-id-metadata/blob/master/sampleTemplate.xls) for ESS-DIVE to provide information about samples that will help make them more discoverable and usable. General fields to describe sample types and locations are required where relevant. Guidance on specific fields were originally developed by SESAR, and modified in some cases by ESS-DIVE. See our [sample metadata guide](https://github.com/ess-dive-community/essdive-sample-id-metadata/blob/master/guide.md) for descriptions and instructions for each metadata field.
+Complete the [sample template](sampleTemplate.xls) for ESS-DIVE to provide information about samples that will help make them more discoverable and usable. General fields to describe sample types and locations are required where relevant. Guidance on specific fields were originally developed by SESAR, and modified in some cases by ESS-DIVE. See our [sample metadata guide](guide.md) for descriptions and instructions for each metadata field.
 
 ## When do you need IGSNs
 
@@ -53,8 +53,9 @@ Here are instructions on how to register your ESS samples for IGSNs through SESA
 
 7. When the relevant sample analyses are completed for a data package, submit your sample metadata and data to ESS-DIVE. ESS-DIVE will be developing tools to enable advanced search for samples using IGSNs, and linking samples to other related samples, datasets and publications.
 8. Update your sample metadata when datasets are published by adding links to related datasets and publications, as a “Related URL” along with a “URL Description”.
+9. Within the FLMD file, the [standard](https://github.com/ess-dive-workspace/essdive-file-level-metadata/blob/main/flmd_quick_guide.md#standard) for each sample ID and metadata reporting format related file should be **ESS-DIVE Sample v1**. If submitting your dataset to ESS-DIVE, include the keyword **ESS-DIVE Sample ID and Metadata Reporting Format** in the package-level metadata.
 
 ## Provide Feedback
 
-We will continue to work with the ESS community to improve the representation of ESS samples in standard sample metadata relevant across a variety of biological and geological samples. Please [contribute](contribute.md) by submiting issues, using our issue templates, or contact ess-dive-support@lbl.gov to provide any feedback on the process of registering samples for IGSNs, specific metadata fields or controlled vocabulary terms.
+We will continue to work with ESS researchers to improve the representation of ESS samples in standard sample metadata relevant across a variety of biological and geological samples. Please [contribute](contribute.md) by submiting issues, using our issue templates, or contact ess-dive-support@lbl.gov to provide any feedback on the process of registering samples for IGSNs, specific metadata fields or controlled vocabulary terms.
 #
