# BH22 - Project 25 meeting minutes

## Scientific and technical enhancement of bioinformatics software metadata using the Tools Ecosystem open infrastructure

### Meeting with Erik Jaaniso

Questions:

- Check for a methodological bias example if it wants to cover all topics are not. All topics are used in edam, is there a reason based on pub2tool?

- Can you annotated with auxialirray concept? are th auxiliray concept used only from "manual" annotation?
Erik answer

> So, about the auxiliary concepts. The short answer is, that currently Pub2Tools and EDAMmap sometimes do output some of the auxiliary concepts and never output some of the other auxiliary concepts.
>
> I understand, that the auxiliary concepts are those in EDAM_1.25.owl that have the property:
> <notRecommendedForAnnotation>true</notRecommendedForAnnotation>
>
> Currently, I'm not checking for this property. Rather, there is a hardcoded list of (auxiliary/organisational) concepts, that should never be mapped to in EDAMmap. There is this related Github issue: https://github.com/edamontology/edammap/issues/4.
>
> That is, all auxiliary concepts present in the file https://github.com/edamontology/edammap/blob/master/core/src/main/resources/edam/blacklist.txt are never output. But, in the the newest EDAM, there are some more auxiliary concepts (marked with <notRecommendedForAnnotation>true</notRecommendedForAnnotation>), that have not been added to the blacklist.txt file. So the following auxiliary concepts can still be output by EDAMmap:
> http://edamontology.org/operation_0337 (Visualisation)
> http://edamontology.org/operation_2409 (Data handling)
> http://edamontology.org/operation_2425 (Optimisation and refinement)
> http://edamontology.org/operation_2426 (Modelling and simulation)
> http://edamontology.org/operation_2428 (Validation)
> http://edamontology.org/operation_2429 (Mapping)
> http://edamontology.org/operation_3432 (Clustering)
> http://edamontology.org/operation_3799 (Quantification)
>
> So, in essence, it's a bug. Thanks for finding it. I think I will soon update Pub2Tools/EDAMmap, because Pub2Tools does web scraping of journal articles and over time some of this scraping starts to fail (because publishers change their web page code), so over time the quality of Pub2Tools drops a bit. Which means these web scraping rules need updating from time to time. When I'll do it, I'll also make it so, that these 8 auxiliary concepts above are not output by EDAMmap.
>
> Regards,
> Erik

- Date of the first entries? Formats lack of usage, because of older tools not being annotated?

### 15/11/2022 - Visualization

#### 1) EDAM concept usage within bio.tools - pizza diagram (a.k.a. Pie chart)

Needed queries:

EDAM: For each sub-ontology D|F|O|T
- a) All non obsolete (all subClassOf D|F|O|T)
- b) All obsolete (based on URI)
- c) All new (subClass of ; created_in 1.26)
- d) All auxilliary (subClass of ; notRecommendedForAnnotation true)

Bio.tools:
- e) Used (count all used D|F|O|T)
- f) Obsolete used (ditto ; owl:deprecated true)
- g) Auxilliary used (ditto ; notRecommendedForAnnotation true)

Figure:
used valid = e - f - g
used aux = g
unused aux = d - g
unused valid stable = a - c - d - e + f + g
new = c
unused obsolete = b - f
used obsolete = f

total:
a + b =?= (~~e~~ ~~- f~~ ~~- g) + g~~ ~~+ (d~~ ~~- g~~) + (a ~~- c~~ ~~- d~~ ~~- e~~ ~~+ f~~ ~~+ g~~) ~~+ c~~ + (b ~~- f~~) ~~+ f~~

:warning:
As of the 15/11/2022 one concept is both aux and deprecated (virus identifier data_2913). The valid Virus identifier is data_2785.

It is not used in bio.tools.

If this +-1 will cause trouble, let's remove the "notRecommendedForAnnotation" tag from data_2913, as a hot-fix.
:warning:

#### 2) Annotation of bio.tools query - Venn diagramm and Upset plot

#### 3) Relation consistency between EDAM and Bio.tools

### 10/11/2022

Participants: Hervé, Jennifer, Johan, Hans, Tomas, Magnus, Adrian, Dmitry, Lucie, Radka

Ask Alban about the missing formats there are only the first ones.

Talk with Johan (mapping between galaxy and bio.tools) and Finn (retreival of tags on rom the workflow hub workflows), promissing.

Dmitry : `curl -H "Accept: application/ld+json" https://openebench.bsc.es/monitor/tool/`

Adding workflow ID in bio.tools as well as adding bio.tools id/dependency to workflow hub

Regarding not recommended EDAM terms from Tomas
- the `Data` concept makes sense to have if it formats are also there (i.e. the user did not know what data type to add , but did know what formats to add). If formats are not there then "Data" makes no sense to keep
- the `Format` makes no sense to have an should be removed

### graphical representation

What part of edam is used in bio.tools divided by subontology?

### 9/11/2022

Participants: Dmitry, Johan, Radka, Tomas, Magnus, Lucie Jennifer, Hervé, Adrian

##### Minutes:

**BHF2F**: worked on the simple queries. Most simple queries have been push on the main repo (good start example).
:warning: WE ALL NEED TO RELOAD EDAM AND BIO.TOOLS because the bio.tools file change. You can deleted and recreate a new repository with the same name.

Serialization of Johan's work (workflow hub/galaxy/bio.tools metadata mining). We discussed with Alban and the bioscemas guys, we have a json format to save this data (see link in the PR#5)

Start of a template to present the work from this project on BioHackrXiv (need for evryone to provide name, affiliation, and ORCID).

Radka demand: Repartition of the work. Work on some plan to assign the free tasks

Still a bug in the bio.tools bioschema dump. We are missing some formats (we'll work on it but it shouldn't change much)

### 8/11/2022

Johan presented his work on workflow hub metadata/galaxy workflows.
Get from workflow hub galaxy tool for each step and then bio.tools id for each galaxy tool.
Question: output format for this data. The best would be to have it as rdf file. Using bioschemas?
Ask around for help for serialization.
Needed info: workflow id, step id/galaxy id , bio.tools id

Questions that should be answered:

| Question | Assigned to | notebook | status |
| -------- | -------- | -------- | ---------- |
| Total non-obsolete operations ||`operation_0004`| 537 🐙
| How many EDAM operations are used to annotate bio.tools? | Lucie | operation_queries.ipynb| 546 (-20 deprecated -1 root) :heavy_check_mark: |
| How many bio.tools entries are annotated with EDAM operations? | Lucie |operation_queries.ipynb | 25228 :heavy_check_mark: |
| How many bio.tools entries are annotated with deprecated operations? Or annotated with edam root operation concept? | Lucie | operation_queries.ipynb| 20, 9 :heavy_check_mark: |
| Total non-obsolete topics in EDAM ||`topic_0003`| 277 🐙
| How many EDAM topics are used to annotate bio.tools? | Jennifer |topics_queries.ipynb | 264 :heavy_check_mark: |
| How many bio.tools entries are annotated with EDAM topics? | Jennifer | topics_queries.ipynb| 26090 :heavy_check_mark: |
| How many bio.tools entries are annotated with deprecated topics? Or annotated with edam root topic concept? | Jennifer |topics_queries.ipynb |10, 1 :heavy_check_mark: |
| Total non-obsolete data in EDAM ||`data_0006`| 947 🐙
| How many EDAM data are used to annotate bio.tools? | Hervé | data_queries.ipynb | 559 (-18 -1) :heavy_check_mark: |
| How many bio.tools entries are annotated with EDAM data? only input, only output, both :warning:| Hervé | data_queries.ipynb | 3284 (i3172,o2764) :heavy_check_mark: |
| How many bio.tools entries are annotated with deprecated data? Or annotated with edam root data concept? | Hervé | data_queries.ipynb, matus_query_graphdb.ipynb#How-many-bio.tools-entries-are-annotated-with-the-root-"Data"-concept-(input-or-output)? | 163, 339 (1080-times) |
| Total non-obsolete formats in EDAM ||`format_1915`| 618 🐙
| How many EDAM formats are used to annotate bio.tools? | Matus | matus_query_graphdb.ipynb | 254 (-0) :heavy_check_mark: |
| How many bio.tools entries are annotated with EDAM formats? only input, only output, both :warning:| Matus | matus_query_graphdb.ipynb | 2484 (i2223,o1984) :heavy_check_mark: |
| How many bio.tools entries are annotated with deprecated format? Or annotated with edam root format concept? | Matus| matus_query_graphdb.ipynb | 0, 10 (24-times) :heavy_check_mark: |
| How many bio.tools entries have non-recommended EDAM topics +listing | Tomáš, Radka | NotRecommendedForAnnotation.ipynb| 1 :heavy_check_mark: |
| How many bio.tools entries have non-recommended EDAM operations +listing | Tomáš, Radka | NotRecommendedForAnnotation.ipynb |6981 :heavy_check_mark: |
| How many bio.tools entries have non-recommended EDAM data (input, output) +how many/which are EDAM identifiers +listing | Tomáš, Radka | NotRecommendedForAnnotation.ipynb| 1455 annotations :heavy_check_mark: |
| How many bio.tools entries have non-recommended EDAM formats (input, output) +listing | Tomáš, Radka | NotRecommendedForAnnotation.ipynb | 651 annotations :heavy_check_mark: |
| How many EDAM data and formats combinations are in Bio.tools? | Matúš | matus_query_graphdb.ipynb | 6953 (2484 tools) :heavy_check_mark: |
| How many EDAM data and formats combinations are consistent with the is_format_of relation? +listing | Matúš | matus_query_graphdb.ipynb | 1121 (612 tools) :heavy_check_mark: |
| Number of EDAM formats with an _is_format_of_ relation (transitive); and how many have multiple _is_format_of_ relations | Matúš / Lucie | matus_query_graphdb.ipynb | 533, 172 👾
| How many bio.tools entries and inputs/outputs have EDAM formats ~~which are not consistent~~ without the corresponding _is_format_of_ data~~relation~~? +listing | Matúš | | 🧐 |
| Number of EDAM concepts (data, operations) with a _has_topic_ relation (transitive); and how many have multiple _has_topic_ relations | | | 618, 344 👾
| How many bio.tools entries have EDAM topics and operations? | Jennifer | | 25096 :heavy_check_mark:|
| How many bio.tools entries have EDAM topics and operations which are consistent with the _has_topic_ relation? +listing | Adrian | | 21031 |
| How many bio.tools entries have EDAM topics and operations which are not consistent with the _has_topic_ relation? +listing | | | |
| How many bio.tools entries have EDAM data and topics? |Jennifer | |3245 (for input and/or output) :heavy_check_mark: |
| How many bio.tools entries have EDAM data and topics which are consistent with the _has_topic_ relation? +listing | | | |
| How many bio.tools entries have EDAM data and topics which are not consistent with the _has_topic_ relation? +listing | | | |
| How many bio.tools entries have EDAM operations and data? |Jennifer | |3284(for input and/or output):heavy_check_mark: |
| Number of EDAM operations with a _has_input_ relation (transitive); and how many have multiple _has_input_ relations | | | 292, 74 👾
| How many bio.tools entries have EDAM operations and data which are consistent with the _has_input_ relation? +listing | | | |
| How many bio.tools entries have EDAM operations and data which are not consistent with the _has_input_ relation? +listing | | | |
| Number of EDAM operations with a _has_output_ relation (transitive); and how many have multiple _has_output_ relations | | | 293, 97 👾
| How many bio.tools entries have EDAM operations and data which are consistent with the _has_output_ relation? +listing | | | |
| How many bio.tools entries have EDAM operations and data which are not consistent with the _has_output_ relation? +listing | | | |
|How many relations _has_topic_ are redundant in EDAM (declared in parent+ and children concept) +listing||||
|How many relations _has_output_ are redundant in EDAM (declared in parent+ and children concept) +listing||||
|How many relations _has_input_ are redundant in EDAM (declared in parent+ and children concept) +listing||||
|How many relations _is_format_of_ are redundant in EDAM (declared in parent+ and children concept) +listing||||
|How many subClassOf relations are redundant in EDAM? +listing ||||
|How many tools are redundant in bio.tools for operation? (annotated within the same operation with a concept and its parents)||||
|How many tools are redundant in bio.tools for topic? (annotated with a topic and its parents)||||
|How many inputs/outputs/tools are redundant in bio.tools for format? (annotated with a format and its parents)||||

- Get info on tools from github repo
- check for spam tools (just name, home page , description) minimal requierements
- model [bio.tools](http://bio.tools) data as a library (where you validate data outside the bio.tools) bio.tools python lib pydantic

### 7/11/2022

**Present:** Lucie, Jennifer, Hans, Dmitry, Johan, Radka, Magnus, Matus, Hervé, Tomas Racek

- Daily meeting in the project 25 break out room (https://elixir-europe-org.zoom.us/j/84668354125?pwd=dGhZbFhCSXFheWtYYWNEMkJSanZBUT09#success) 9:30-10:30 am.
- Book "Indianapolis" room everyday 9:00-10:30
- Ask for an owl everyday (only fair to get an OWL to hack OWL)
- Decide and add a license

https://github.com/bio-tools/biohackathon2022

### 20/10/2022

#### Participants:
Magnus, Jennifer, Lucie, Matúš, Hervé, Hans

Agenda:
- Add ressources to [Available_ressources.md](https://github.com/elixir-europe/biohackathon-projects-2022/blob/main/25/Available_ressources.md)
- Communicate with slack from now on?
- Work environment

Available ressources: we can reuse [code](https://github.com/bio-tools/biohackathon2021) from last year biohackathon.

Aksing bh team give rights to the github.

Confirmation, from now on we use the slack channel (invite Veit and Anna-Lena)

Work envronement: @hans remark = what about people who can't write SPARQL?? Jennifer for example. chek out an alternative to sparql, with json for example.

Note from hans to alban: input and output mixed up

have a turtle version of edam and bio.tool!

### 06/10/2022

meeting link : https://cnrs.zoom.us/j/92487858648?pwd=WWM1d3h4WGU1SjlJcVBPV2gxaGdSQT09
Link to the elixir bh repo : https://github.com/elixir-europe/biohackathon-projects-2022/tree/main/25

#### Participants:
Magnus, Jennifer, Veit, Lucie, Alban, Johan, Matúš, Hervé

**In BH physically:** Jennifer, Lucie, Alban (co-lead Bioschemas project), Matus, Hervé
**Virtually**: Magnus, Veit (partly), Johan (jet-lagging😉)

#### Agenda:
Presentation of each participants (their work on EDAM/bio.tools)
Review of the project submission
Work environment during bh
Next meeting?

#### Minutes
Round table

Review of the project submission
The project it still relevant today,the need for this comparison and queries on edam/bio.tools is still present.

##### Prepare before BH (here a brief list, see details & ideas below)
[Alban, Hervé] Access to query bio.tools, EDAM, optionally other resources
[Alban, Lucie] Working environments for us, on local or ideally online. So that we can clone & experiment w/o hassle
[Matus, Alban] List of projects and people at BH (in-situ or virtual) we want to coordinate with
[Everyone] List of resources and links (for us and for others/newcomers)
[Lucie] Paste this doc into HackMD, give access to our GitHub handles, link from https://github.com/elixir-europe/biohackathon-projects-2022/tree/main/25
[Lucie] Onboarding meetup with Jennifer: GitHub account, Gitter, etc. everything (ask Matus if any help/input needed)

##### Work environment during bh
- Access to query bio.tools and EDAM → https://github.com/bio-tools/content/blob/master/doc/bioschemas.md
- Could we query the whole Tools Ecosystem/Universe too?
- Hard to do .. not the same language, no query system …
- Bioschemas Tools Profile?
- An optional nice-to-have would be the possibility to query at least Galaxy IUC/ToolShed/IWC, BIII, and the WorkflowHub (if anyone wants to contribute – the communities will be there at BH!!!)
- Workflows from WorkflowHub -> doable to have an RDF subset
- IWC workflows -> galaxy ()
- list on all available resources, piece of code (on the bh project github)
- See https://github.com/bio-tools/biohackathon2021 for the code and notebooks developed during the - 2021 BioHackathon in the “Making bio.tools fit for workflows” project. This includes notebooks to collect and visualize statistics from bio.tools.
- SPARQL endpoint + query catalog https://github.com/bio-tools/content/blob/master/doc/bioschemas.md
- https://github.com/galaxyproject/iwc/tree/main/workflows

- get the 200+ wf from workflow hub as a queryable rdf?
- What do we need for this? workflowfinder already queries WfH - unsure if any of this is useful? https://github.com/AustralianBioCommons/australianbiocommons.github.io/blob/master/finders/workflowfinder.py
- ALIGNMENT BETWEEN BH PROJECTS: OURS, BIOSCHEMAS, GALAXY/RO-CRATE/IW/WORKFLOWHUB – this will be the ideal use of the BH setup
- https://australianbiocommons.github.io/2_1_workflows.html: they used the workflow hub api to get all the wfh info.
- https://github.com/galaxyproject/iwc/tree/main/workflows: IWC workflows
- when trying to get a wf degistry= be able to identify gaps (when the are some edam missing annotation)
- CWL repo?
- Make a list of the communities present at the BH and prepare to engage with them
- Is it other communities as well? Or just BH?

- Have a working environment to freely experiment and query edam and bio.tools. Online? Local setup? Notebook(s)?
- Have a Jupyter hub. Ask Christophe Blanchet? Alban can take care of it? Who can host? graph db can be deployed locally easily. Binder (cloud solution that hosts notebook)
- A need for different knowledge graph for people to work on separate data sets.

https://workflowhub.eu/workflows.json