@@ -293,6 +293,10 @@ animal associated gut or fecal content
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@@ -293,6 +293,10 @@ animal associated gut or fecal content
Biology is highly contextual (few rules, many exceptions), meaning [context]{.orange} is the key point to address to make data travel across research investigations.
Biology is highly contextual (few rules, many exceptions), meaning [context]{.orange} is the key point to address to make data travel across research investigations.
Why should you share this information?
## Rationale
## Rationale
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@@ -359,7 +363,9 @@ MIxS lists three *mandatory* environmental metadata fields that expect [ontology
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@@ -359,7 +363,9 @@ MIxS lists three *mandatory* environmental metadata fields that expect [ontology
## Focusing on biological and environmental metadata
## Focusing on biological and environmental metadata
What can you tell us about the biological & environmental provenance of your dataset or sample?
What can you tell us about the biological & environmental provenance of your dataset or sample?
Were are your samples from? Do you use a model organism?
Where are your samples from? Do you use a model organism?
How can you make this information machine-accessible?
## Why bother with ontologies?
## Why bother with ontologies?
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@@ -368,7 +374,7 @@ Were are your samples from? Do you use a model organism?
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@@ -368,7 +374,7 @@ Were are your samples from? Do you use a model organism?
- improve machine-readability of your datasets
- improve machine-readability of your datasets
- help others correctly categorize & re-use your datasets > [recontextualization]{.orange}
- help others correctly categorize & re-use your datasets > [recontextualization]{.orange}
- required by data repositories
- required by data repositories
- first step towards open linked data and knowledge graph representations?
- first step towards open linked data and knowledge graph representations
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# Having fun with ontologies
# Having fun with ontologies
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@@ -392,7 +398,7 @@ Let's talk about...
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@@ -392,7 +398,7 @@ Let's talk about...
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- Were you thinking of the baked goods, such as [`cake [ENVO:02000063]`](http://purl.obolibrary.org/obo/ENVO_02000063)?
- Were you thinking of the baked goods, such as [`cake food product [FOODON:00001278]`](http://purl.obolibrary.org/obo/FOODON_00001278)?
- unfortunately there was no well described ontology term for [`pie`](http://purl.obolibrary.org/obo/FOODON_00002476)
- unfortunately there was no well described ontology term for [`pie`](http://purl.obolibrary.org/obo/FOODON_00002476)
- Or were you thinking of the [`pie [44315]`](http://identifiers.org/ncbigene/44315) gene that encodes the [`pineapple eye protein (fruit fly) [PR:Q9VKW2]`](http://purl.obolibrary.org/obo/PR_Q9VKW2)?
- Or were you thinking of the [`pie [44315]`](http://identifiers.org/ncbigene/44315) gene that encodes the [`pineapple eye protein (fruit fly) [PR:Q9VKW2]`](http://purl.obolibrary.org/obo/PR_Q9VKW2)?
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@@ -657,7 +663,7 @@ Get more help on [ENVO's wiki page about microbial samples](https://github.com/E
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@@ -657,7 +663,7 @@ Get more help on [ENVO's wiki page about microbial samples](https://github.com/E
- Sample: feces collected in the wild
- Sample: feces collected in the wild
- Model system: Eurasian river otter (*Lutra lutra*)
- Model system: Eurasian river otter (*Lutra lutra*)
> See the "full" methods section in the [pad](https://pad.carpentries.org/2024-07-18-biometadata-02-learners)!
> See the "full" methods section in the [pad](https://pad.carpentries.org/2024-12-04_Biometadata-crashcourse)!
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@@ -678,7 +684,7 @@ Image by Bernard-Boehne from [Wikimedia Commons](https://commons.wikimedia.org/w
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@@ -678,7 +684,7 @@ Image by Bernard-Boehne from [Wikimedia Commons](https://commons.wikimedia.org/w
- **Go** to <https://data-sandbox.microbiomedata.org/submission/>
- **Go** to <https://data-sandbox.microbiomedata.org/submission/>
- **Log** with your ORCID and go again to the link above
- **Log** with your ORCID and go again to the link above
- **Create** a new submission using the otter dataset
- **Create** a new submission using the otter dataset
- **Read** the methods section in the [pad](https://pad.carpentries.org/2024-07-18-biometadata-02-learners)
- **Read** the methods section in the [pad](https://pad.carpentries.org/2024-12-04_Biometadata-crashcourse)
- **Download** the [XLSX template](https://git.rwth-aachen.de/clavellab/workshop-biometadata-03/-/raw/main/lectures/template_marcel.xlsx?ref_type=heads&inline=false) to help you validate your submission
- **Download** the [XLSX template](https://git.rwth-aachen.de/clavellab/workshop-biometadata-03/-/raw/main/lectures/template_marcel.xlsx?ref_type=heads&inline=false) to help you validate your submission