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feat (im): refined dropdown items, repaired links, standardized forma…
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njlyon0 committed Nov 19, 2024
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26 changes: 10 additions & 16 deletions _quarto.yml
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Expand Up @@ -24,25 +24,19 @@ website:
href: im/new-to-lter.qmd
- text: "New to IM"
href: im/new-to-im.qmd
- text: "EML"
href: im/eml.qmd
- text: "GitHub Organizations"
href: im/github-organization-recs.qmd
- text: "Site Identifier"
href: im/site-identifier.qmd
- text: "Site Personnel"
- text: "Get Help"
href: im/getting-help.qmd
- text: "Update People"
href: im/site-personnel.qmd
- text: "Site Publications"
- text: "Update Pubs"
href: im/site-publications.qmd
- text: "Site Websites"
- text: "Websites"
href: im/site-websites.qmd
- text: "Bibtex"
href: im/bibtex.qmd
- text: "Biblio Fields"
href: im/biblio-fields.qmd
- text: "Getting Help"
href: im/getting-help.qmd
- text: "Editing IM Docs"
- text: "Write EML"
href: im/eml.qmd
- text: "Site GitHub Orgs"
href: im/github-organization-recs.qmd
- text: "Suggest Edits"
href: im/edits.qmd
right:
- icon: github
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26 changes: 8 additions & 18 deletions im/eml.qmd
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@@ -1,42 +1,32 @@
---
title: "Ecological Metadata Language (EML)"
title: "Creating EML"
format: html
---

## Creating EML

The [Ecological Metadata Language (EML)](https://eml.ecoinformatics.org/) is an XML schema for describing ecological datasets.
EDI maintains [best practices for EML](https://ediorg.github.io/data-package-best-practices/) that you should review when writing your own EML.

There are many one-off solutions for creating EML at LTER sites. Some common ones are listed below, as well as some newer offerings from EDI.
The [Ecological Metadata Language (EML)](https://eml.ecoinformatics.org/) is an XML schema for describing ecological datasets. EDI maintains [best practices for EML](https://ediorg.github.io/data-package-best-practices/) that you should review when writing your own EML. There are many one-off solutions for creating EML at LTER sites. Some common ones are listed below, as well as some newer offerings from EDI.

## ezEML

[ezEML](https://ezeml.edirepository.org) is an online form based EML editor.
ezEML has developed into a very simple approach for generating metadata files at three levels:

* If you're starting from scratch or don't have much experience with metadata.
* If you need to gather metadata from a researcher or student at your site, you can let them start from a template that you have created.
* Set ezEML up for your site's metadata management:
+ Import EML snippets from other files. This option lets you set up something akin to a metadata database from which to import parts needed for a new EML file.
+ Import datapackages (EML and data) from the EDI repository for updates and new versions.
- If you're starting from scratch or don't have much experience with metadata.
- If you need to gather metadata from a researcher or student at your site, you can let them start from a template that you have created.
- Set ezEML up for your site's metadata management:
- Import EML snippets from other files. This option lets you set up something akin to a metadata database from which to import parts needed for a new EML file.
- Import datapackages (EML and data) from the EDI repository for updates and new versions.

Extensive documentation may be found in the [user guide](https://ezeml.edirepository.org/eml/user_guide) or on [YouTube](https://www.youtube.com/playlist?list=PLi1PZkcSXdAKTtpgyHnd8GjtL6kRMMGFR).


## LTER Core Metabase

Some LTER sites manage dataset metadata using a Postgres database schema called [Metabase](https://github.com/lter/LTER-core-metabase).
It is maintained by LTER IMs, as is the companion R code called [MetaEgress](https://github.com/BLE-LTER/MetaEgress) for generating EML from Metabase.
The original Metabase was developed at GCE, but the current version (called LTER Core Metabase) is in use at BLE and JRN.

Some LTER sites manage dataset metadata using a Postgres database schema called [Metabase](https://github.com/lter/LTER-core-metabase). It is maintained by LTER IMs, as is the companion R code called [MetaEgress](https://github.com/BLE-LTER/MetaEgress) for generating EML from Metabase. The original Metabase was developed at GCE, but the current version (called LTER Core Metabase) is in use at BLE and JRN.

## EMLassemblyline

[EMLassemblyline](https://ediorg.github.io/EMLassemblyline/) is an R package for creating EML.
It is maintained by EDI and is used by several LTER sites such as HBR, JRN, NES, and NTL.


## DEIMS

DEIMS used to be a [Drupal](https://www.drupal.org/)-based solution for LTER websites. Drupal is a flexible content management system / programming environment that supports metadata based LTER websites well due to its database backend. It can also be used to generate EML. Recent efforts of upgrading from the original DEIMS to Drupal 8/9 are well documented in this [GitHub repository](https://github.com/lter/Deims7-8-Migration) and modules for extracting and ingesting metadata have been developed.
8 changes: 3 additions & 5 deletions im/getting-help.qmd
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Expand Up @@ -3,14 +3,12 @@ title: "Getting IM Help"
format: html
---

For general information management (IM) questions, check out the **im** channel in the [LTER Slack workspace](https://lter.slack.com/).
For general information management (IM) questions, check out the **`#im`** channel in the [LTER Slack workspace](https://lter.slack.com/).
Post your question, and you'll likely get a response from other IMs active that day.

For general LTER questions, again try [Slack](https://lter.slack.com/), or just [email Marty Downs](mailto:[email protected]), director of the LTER Network Office (LNO).
If Marty gets tired of the spam, be sure to point her to this page so she can edit it and scold Tim for posting her address.
For general LTER questions, again try [Slack](https://lter.slack.com/), or email director of the LTER Network Office (LNO) Marty Downs.

For help with archiving data at the Environmental Data Initiative, [email EDI](mailto:[email protected]). Or join [EDI's Slack](https://edi-got-data.slack.com).
They are generally very responsive and helpful.

If you see something at an LTER site and you want to know how they did that, reach out to the IM. We're a friendly community.
Some are even eager to share because shared solutions can be more sustainable and it makes the site look good when reviews and renewals come up!
If you see something at an LTER site and you want to know how they did that, reach out to the IM. We're a friendly community. Some are even eager to share because shared solutions can be more sustainable and it makes the site look good when reviews and renewals come up!
3 changes: 1 addition & 2 deletions im/github-organization-recs.qmd
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Expand Up @@ -13,7 +13,7 @@ The LTER Network has followed our own advice and has a GitHub Organization which

## Naming Convention

We recommend adopting a common organization naming convention so that visitors to one organization can easily find the organization of another LTER site. Six sites currently have organizations and the general naming convention is to use the three letter site abbreviation in all caps followed by a hyphen and "LTER" (e.g., "JRN-LTER").
We recommend adopting a common organization naming convention so that visitors to one organization can easily find the organization of another LTER site. Six sites currently have organizations and the general naming convention is to use the three letter site abbreviation in all caps followed by a hyphen and "LTER" (e.g., "MSP-LTER").

Note that organization names can be changed as needed without breaking an individual user's code but the link to GitHub-hosted websites/etc. will be changed if the organization name changes.

Expand Down Expand Up @@ -56,4 +56,3 @@ The [Beaufort Lagoon Ecosystem GitHub Organization](https://github.com/BLE-LTER)
## GitHub Organization vs. Other Platforms

If you are already using a comparable non-GitHub platform (e.g., [BitBucket](https://bitbucket.org/product), [GitLab](https://about.gitlab.com/), etc.) we still recommend creating a GitHub Organization! At the very least, an organization for your site will give site researchers who do use GitHub a place to store their code and interact with peers who also use GitHub–both at and outside of your site. You can also use the description field of your organization to direct visitors to the link of whichever alternate platform your site decides best fits your needs. Finally, if a majority of sites do create their own organizations, external users will be able to use the standard naming convention to navigate among sites even in cases where each site utilizes the organization at different levels of intensity.

22 changes: 11 additions & 11 deletions im/home.qmd
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Expand Up @@ -7,17 +7,17 @@ This part of the website is a place for new and experienced LTER information man

This facet of the website gathers the current practices and procedures that apply to information management **within the LTER Network** in one place. It does not aspire to be a single source of information and resources for information management more generally--nor even for the myriad best practices that have been established through IM collaboration in the LTER Network.

Any LTER information manager may make edits to these pages, but it is likely to be most actively updated by the LTER Network Office and the LTER IM Executive Team. All LTER Information Managers will want to "watch" the repo for updates or check back regularly. To view the source code for any of these pages, see [here](https://github.com/lter/docs-network/tree/main/im). For specific procedures on making edits to the manual, please see [CONTRIBUTING.md](https://github.com/lter/docs-network/blob/main/CONTRIBUTING.md).
Any LTER information manager may make edits to these pages, but it is likely to be most actively updated by the LTER Network Office and the LTER IM Executive Team. All LTER Information Managers will want to "watch" the repo for updates or check back regularly. To view the source code for any of these pages, see [here](https://github.com/lter/docs-network/tree/main/im).

### What Do You Need to Do?

- [I'm brand new to LTER](http://lter.github.io/im-manual/new-to-lter)
- [I'm familiar with LTER, but a new Information Manager](http://lter.github.io/im-manual/new-to-im)
- [Ask for help with something](http://lter.github.io/im-manual/getting-help)
- [Update my site's personnel](http://lter.github.io/im-manual/site-personnel)
- [Update my site's publications](https://lter.github.io/im-manual/site-publications)
- [Obtain a unique site identifier](https://lter.github.io/im-manual/site-identifier)
- [Create (or edit) a site website](https://lter.github.io/im-manual/site-websites)
- [Write Ecological Markup Language (EML)](https://lter.github.io/im-manual/eml)
- [Establish a site GitHub Repository](github-organization-recs.md)
- [Suggest edits to the IM Manual](https://lter.github.io/im-manual/edits)
- [I'm brand new to LTER](https://lter.github.io/docs-network/im/new-to-lter.html)
- [I'm familiar with LTER, but a new Information Manager](http://lter.github.io/docs-network/im/new-to-im.html)
- [Ask for help with something](http://lter.github.io/docs-network/im/getting-help.html)
- [Update my site's personnel](http://lter.github.io/docs-network/im/site-personnel.html)
- [Update my site's publications](https://lter.github.io/docs-network/im/site-publications.html)
- [Obtain a unique site identifier](https://lter.github.io/docs-network/im/site-identifier.html)
- [Create (or edit) a site website](https://lter.github.io/docs-network/im/site-websites.html)
- [Write Ecological Markup Language (EML)](https://lter.github.io/docs-network/im/eml.html)
- [Establish a site GitHub Organization](https://lter.github.io/docs-network/im/github-organization-recs.html)
- [Suggest edits to the IM Manual](https://lter.github.io/docs-network/im/edits.html)
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