Merge branch 'main' of https://github.com/digital-botanical-gardens-i…

…nitiative/dendron-dbgi

vault/Master-Works.Edouard-Brülhart.Collection.md

@@ -0,0 +1,7 @@
+---
+id: i6scy8dy7a9appqdqvxas6j
+title: Collection
+desc: ''
+updated: 1718557537307
+created: 1718557537307
+---

vault/Master-Works.Edouard-Brülhart.Database.md

@@ -6,9 +6,9 @@ updated: 1718358903442
 created: 1718349400476
 ---
 
-## [[Master-Works.Edouard-Brülhart.Database.Services.Directus]]
+## [[Master-Works.Edouard-Brülhart.Services.Directus]]
 
-The database we use is an integration of [[Master-Works.Edouard-Brülhart.Database.Services.PostgreSQL]], a robust relational database system, with [[Master-Works.Edouard-Brülhart.Database.Services.Directus]], an open-source data platform. The combined solution offers a powerful, flexible, and user-friendly environment for managing structured data. This setup enables efficient data storage, retrieval, and management with a modern web-based interface, suitable for diverse applications in scientific research and beyond."
+The database we use is an integration of [[Master-Works.Edouard-Brülhart.Services.PostgreSQL]], a robust relational database system, with [[Master-Works.Edouard-Brülhart.Services.Directus]], an open-source data platform. The combined solution offers a powerful, flexible, and user-friendly environment for managing structured data. This setup enables efficient data storage, retrieval, and management with a modern web-based interface, suitable for diverse applications in scientific research and beyond."
 
 This database is the core part that stores the data from the beginning to the end. This then permits to retrieve easily and automatically all necessary metadata coming from the different services we use.
 

vault/Master-Works.Edouard-Brülhart.Laboratory.md

@@ -0,0 +1,7 @@
+---
+id: 4u9167irz9kzo0w3noogs2t
+title: Laboratory
+desc: ''
+updated: 1718557636202
+created: 1718557636202
+---

vault/Master-Works.Edouard-Brülhart.Mass-spectrometry.md

@@ -0,0 +1,7 @@
+---
+id: gt1q9bzu5eep82sxxog219k
+title: Mass spectrometry
+desc: ''
+updated: 1718557600639
+created: 1718557586154
+---

vault/Master-Works.Edouard-Brülhart.Methods.md

@@ -2,16 +2,18 @@
 id: 5u2uiaco359415r2i31ymac
 title: Methods
 desc: ''
-updated: 1718372787886
+updated: 1718557636314
 created: 1718349372688
 ---
 The methods are organized in four categories, following the chronological order of the workflow.
 
 ### [[Master-Works.Edouard-Brülhart.Database]]
 
-### Collection process
+### [[Master-Works.Edouard-Brülhart.Collection]]
 The collection process is made using QGIS and QField, with a QFieldCloud server.
 
-### Lab process
-### Mass spectrometry process
+### [[Master-Works.Edouard-Brülhart.Laboratory]]
+
+
+### [[Master-Works.Edouard-Brülhart.Mass spectrometry]]
 

vault/open-notebook.dbgi.dtandon.2024.04.15.md

@@ -2,7 +2,7 @@
 id: ig41sdi15e6x9f1o8zaeqwu
 title: '2024-04-15'
 desc: ''
-updated: 1713203654590
+updated: 1718354530862
 created: 1713166208351
 traitIds:
   - open-notebook-dbgi-dtandon
@@ -54,7 +54,7 @@ https://www.science-studios.ch/
 4. #SciComm Build a graphical overview of the two ideas discussed with Manuela.
 
 ## Today I learned that
-1. Ontop with duckdb https://www.linkedin.com/pulse/scaling-sparql-querying-billion-observations-ontop-duckdb-gschwend-myghf/
+1. Ontop with duckdb https://www..com/pulse/scaling-sparql-querying-billion-observations-ontop-duckdb-gschwend-myghf/
 
 ## Paused
 

vault/open-notebook.dbgi.lcappelletti.2023.07.17.md

@@ -2,7 +2,7 @@
 id: twrgu2q3yot15pz1v2en7f6
 title: '17'
 desc: ''
-updated: 1689601789408
+updated: 1718354530867
 created: 1689585522386
 ---
 
@@ -22,11 +22,11 @@ Today is 2023.07.17
 * What you are currently reading is my first entry in Denron DBGI.
 * [BioCypher](https://arxiv.org/abs/2212.13543) and [PheKnowLator](https://arxiv.org/abs/2307.05727) are primarily pipelines in Python for combining KGs. We need an efficient and robust pipeline to **create** a KG from scratch, and first thing first Python is likely not the suitable candidate for such objectives, altough it is okay when one needs to smash things togheter. The objective of the Earth Metabolome KG is not to compose through ETL several existing ontologies and KGs, but to create a new KG from the metabolomic data and its metadata. While it is vital for the long term viability of these data to be compatible with the existing ontologies and graphs by following the naming conventions for species for instance from the likes of [NCBITaxon](https://www.ncbi.nlm.nih.gov/taxonomy), it is not the goal of this KG to ingest them. The Earth Metabolome KG is not a KG of KGs, it is a KG of metabolomic data, that may be included in several other KGs.
 * [KG-Hub](https://academic.oup.com/bioinformatics/article/39/7/btad418/7211646) is similar in nature to the aforementioned libraries, but also provides a [web-hosting that makes it particularly easy to access versioned KGs.](https://kghub.org/) The standardized nature of the node types and edge types through the biolink format make it easier to combine different KGs, thought in several instances the level of detail in the hierarchy of biolink effectively used is too coarse and stops at extremely high level labels such as [biolink:NamedThing](https://biolink.github.io/biolink-model/docs/NamedThing.html). Aiming to have a standardized and structured set of labels will be vital for the Earth Metabolome KG, but they will also need to be finely grained and detailed enough to be useful for the biological samples and metabolomic data. The ease of access and clear versioning of the [KG-Hub](https://academic.oup.com/bioinformatics/article/39/7/btad418/7211646) data is surely something to be imitated. Finally, the tight integration of the [GRAPE](https://github.com/AnacletoLAB/grape) library with [KG-Hub](https://academic.oup.com/bioinformatics/article/39/7/btad418/7211646) is something to be considered for the Earth Metabolome KG.
-* Asked to [Deepak Unni](https://www.linkedin.com/in/deepakunni3/), who is the main author of [BioLink](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9372416/), whether it provides support for biological samples as it is unclear from the BioLink paper and website.
+* Asked to [Deepak Unni](https://www..com/in/deepakunni3/), who is the main author of [BioLink](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9372416/), whether it provides support for biological samples as it is unclear from the BioLink paper and website.
 
 
 ## Todo tomorrow
 * Write an entry describing the benefits of having a hierarchy for the Earth Metabolome KG's node & edge labels. Use [Biolink KG](https://github.com/LucaCappelletti94/kg-biolink) as an example of an effective characterization of metadata based on the metadata topology.
-* Delve into whether the data models suggested by [Chris Mungall](https://www.linkedin.com/in/chrismungall/) are a viable solution for the characterization of biological samples.
+* Delve into whether the data models suggested by [Chris Mungall](https://www..com/in/chrismungall/) are a viable solution for the characterization of biological samples.
 * Bother the authors of the resources that seem to be the most promising for the Earth Metabolome KG so to make sure I am not missing anything and neither reinventing the wheel.
 * Start to delve into the [ENPKG Workflow](https://github.com/enpkg/enpkg_workflow) so as to plan a holystic refactoring, if needed.

vault/open-notebook.dbgi.lcappelletti.2023.07.18.md

@@ -2,7 +2,7 @@
 id: bwu3bavs2hymd3x55ikezub
 title: '17'
 desc: ''
-updated: 1690284260848
+updated: 1718354530885
 created: 1689672762964
 ---
 
@@ -16,7 +16,7 @@ Today is 2023.07.18
 ## Done
 
 ### On Biolink
-[Deepak Unni](https://www.linkedin.com/in/deepakunni3/), who is the main author of [BioLink](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9372416/), said the following regarding the support of BioLink for biological samples:
+[Deepak Unni](https://www..com/in/deepakunni3/), who is the main author of [BioLink](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9372416/), said the following regarding the support of BioLink for biological samples:
 
 > Biolink Model does have a few concepts that can be used to represent information about samples. But I don't think it is sufficiently modelled to support processing of samples as it is done for genomic sequencing or single cell sequencing. Ideally, it would be good to explore how the model can be extended to support this knowledge.
 
@@ -32,5 +32,5 @@ Deepak also pointed me to the following resources:
 The [BioLink](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9372416/) comes equipped with two important features that are oftem under appreciated: the textual description associated to the node and edge labels, and the hierarchy of the node and edge labels. We can create node type and edge type features from the textual features using procedures such as [Okapi BM25-weighted BERT](https://github.com/AnacletoLAB/grape/blob/main/tutorials/BM25_weighted_pretrained_BERT_based_textual_embedding_using_GRAPE.ipynb) and by composing the [BioLink hyerarchy into a KG](https://github.com/LucaCappelletti94/kg-biolink) we can use any node embedding model to get additional topological node type and edge type features. These features can be used for many tasks, such as the classification of the nodes and edges, and the prediction of the edges. The [BioLink](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9372416/) hierarchy is not perfect, but it provides several good inspirations that should be followed for the Earth Metabolome KG.
 
 ## Todo tomorrow
-* Delve into whether the data models suggested by [Chris Mungall](https://www.linkedin.com/in/chrismungall/) are a viable solution for the characterization of biological samples.
+* Delve into whether the data models suggested by [Chris Mungall](https://www..com/in/chrismungall/) are a viable solution for the characterization of biological samples.
 * Start to delve into the [ENPKG Workflow](https://github.com/enpkg/enpkg_workflow) so as to plan a holystic refactoring, if needed.

vault/open-notebook.dbgi.lcappelletti.2023.07.19.md

@@ -2,7 +2,7 @@
 id: 4gh9ubiyqx2c29rph7lyax3
 title: '17'
 desc: ''
-updated: 1689778750988
+updated: 1718354530881
 created: 1689775221469
 ---
 
@@ -31,5 +31,5 @@ git clone [email protected]:enpkg/enpkg_graph_builder.git
 ```
 
 ## Todo tomorrow
-* Delve into whether the data models suggested by [Chris Mungall](https://www.linkedin.com/in/chrismungall/) are a viable solution for the characterization of biological samples.
+* Delve into whether the data models suggested by [Chris Mungall](https://www..com/in/chrismungall/) are a viable solution for the characterization of biological samples.
 * Start writing a test suite for the [data organization](https://github.com/enpkg/enpkg_data_organization/tree/refactoring) repository with the data [made available on Zenodo](https://zenodo.org/record/8152039). 

vault/open-notebook.dbgi.lcappelletti.2023.07.21.md

@@ -2,7 +2,7 @@
 id: qs8zsh67h8a5kj4klmtnxbj
 title: '17'
 desc: ''
-updated: 1689952153135
+updated: 1718354530857
 created: 1689950746986
 ---
 
@@ -51,5 +51,5 @@ The following list of libraries used in the code has been identified, which will
 
 
 ## For next week
-* Delve into whether the data models suggested by [Chris Mungall](https://www.linkedin.com/in/chrismungall/) are a viable solution for the characterization of biological samples.
+* Delve into whether the data models suggested by [Chris Mungall](https://www..com/in/chrismungall/) are a viable solution for the characterization of biological samples.
 * Ask to Pierre-Marie for help understanding how to start using the data [made available on Zenodo](https://zenodo.org/record/8152039) for testing the [data organization](https://github.com/enpkg/enpkg_data_organization/tree/refactoring) and in chain all others to avoid breaking the pipeline during the refactoring.

vault/open-notebook.dbgi.mvisani.2024.02.09.md

@@ -2,7 +2,7 @@
 id: f3wly7juhxjotu33qfw1wvo
 title: '2024-02-09'
 desc: ''
-updated: 1707499094082
+updated: 1718354530890
 created: 1707499015014
 traitIds:
   - open-notebook-mvisani
@@ -25,4 +25,4 @@ Today is 2024.02.09
 
 
 ## Todo on Monday 2024.02.12
-- [ ] **Write LinkedIn post about Sirius binding !!!!**
+- [ ] **Write  post about Sirius binding !!!!**

vault/open-notebook.dbgi.mvisani.2024.02.13.md

@@ -2,7 +2,7 @@
 id: zlzmw93ezh9g89apr3l77zj
 title: '2024-02-13'
 desc: ''
-updated: 1707834918892
+updated: 1718354530876
 created: 1707818340915
 traitIds:
   - open-notebook-mvisani
@@ -15,7 +15,7 @@ Today is 2024.02.13
 ## Notes
 Add time taken to learn the language, tag pma, tag luca
 
-create a linkeding organisation for the EMI 
+create a g organisation for the EMI 
 ## Todo today
 - [ ] 
 

vault/open-notebook.dbgi.mwannier.2023.05.11.md

@@ -2,7 +2,7 @@
 id: pwgi25wmjyo2lw342x3npi6
 title: '2023-05-11'
 desc: ''
-updated: 1683869987093
+updated: 1718354530853
 created: 1683793354813
 traitIds:
   - open-notebook-mwannier
@@ -24,7 +24,7 @@ Today is 2023.05.11
 ## NOTES
 
 Followed a lesson on D3js:
-https://www.linkedin.com/learning/d3-js-essential-training-for-data-scientists/creating-a-linear-scale?autoplay=true
+https://www..com/learning/d3-js-essential-training-for-data-scientists/creating-a-linear-scale?autoplay=true
 
 ## TODO NEXT
 

vault/open-notebook.dbgi.pmallard.2023.06.15.md

@@ -2,7 +2,7 @@
 id: 1n9kw635ospnbwjvismwj9u
 title: '2023-06-15'
 desc: ''
-updated: 1686847854180
+updated: 1718354530872
 created: 1686813851132
 traitIds:
   - open-notebook-dbgi-pmallard
@@ -112,7 +112,7 @@ For next meeting:
 
 Justin Reese indicates these meetings each 2 weeks
 
-https://www.linkedin.com/feed/update/urn:li:activity:7074081027261874176/
+https://www..com/feed/update/urn:li:activity:7074081027261874176/
 
 Topic of negative sampling. A pretty complex topi
 

vault/open-notebook.dbgi.pmallard.2024.06.18.md

@@ -0,0 +1,62 @@
+---
+id: 7s00deq4u6037m0udwo87do
+title: '2024-06-18'
+desc: ''
+updated: 1718701130350
+created: 1718701130350
+traitIds:
+  - open-notebook-dbgi-pmallard
+---
+
+
+# This is PMA's DBGI daily open-notebook.
+
+Today is 2024.06.18
+
+## Todo today
+
+### Have a look at the DBGI discussion forum
+    - https://github.com/orgs/digital-botanical-gardens-initiative/discussions
+###
+###
+
+## Doing
+
+## Paused
+
+## Done
+
+## Notes
+
+Points with Disha on Traits and Globi
+
+Todo :
+
+use pyotl to resolve
+1. wikidata species names
+2. TRYDB species names
+
+Then only proceed to the species names matching.
+
+
+BiotXplorer
+
+https://sibils.text-analytics.ch/
+
+https://sibils.text-analytics.ch/doc/api/fetch/
+
+
+
+
+
+
+## Todo tomorrow, one day ... or never
+
+###
+###
+###
+
+
+## Today I learned that
+
+-