PROJECT NAME: WikiPathways
(PROJECT LONG NAME: WikiPathways + Pathway Figure OCR)
GitHub accounts:
https://github.com/AlexanderPico (lead)
https://github.com/bonohu
https://github.com/RyoNozu
https://github.com/dogrunjp
https://github.com/hiromasaono

Background:
- Despite decades of pathway database and freely available pathway drawing tools, most biologists publish their pathways knowledge as static figures made with PowerPoint. Before the BioHackathon, we identified 103,009 pathway figures in the literature and performed OCR (the [Pathway Figure OCR](https://pfocr.wikipathways.org) project). We extracted human genes, chemicals and disease terms, etc., but we knew that many of the pathways were for plants, microbes and non-model organisms.
- So, during BH23, to expand the pathway analysis environment to non-model organisms whose genomic and functional annotations are not organized in a central public database, we sought to expand the number of organism species included in the PFOCR database. Also, with the goal of expanding the use of [WikiPathways](https://www.wikipathways.org)(ref.1), we thought it necessary to create a video tutorial on how to edit pathway data and add new ones.

Outcomes:
- Expanded species annotations for the Pathway Figure OCR database (Table.1).
* Table　1. The number of new species added to Pathway Figure OCR database in BH23.

| Category | Number of New added Species | Number of Pathways |
|-----------------------------|------------------:|------------------:|
| Plants and Fungi | 9,780 | 25,615 |
| Bacteria | 7,551 | 13,688 |
| Invertebrates | 2,989 | 12,568 |
| Viruses | 1,336 | 10,682 |
| Vertebrates | 1,122 | 9,437 |
| Mammals | 353 | 13,788 |
| Rodents | 162 | 34,766 |
| Phages | 120 | 886 |
| Environmental samples | 112 | 2,438 |
| Primates | 107 | 42,314 |
| Synthetic and Chimeric | 80 | 1,349 |
| **TOTAL** | 23,734 | 167,871* |

\* Including multi-species pathways

- Give a lecture on how to use [PathVisio](https://pathvisio.org), a tool for drawing, editing, and analyzing biological pathways. (pico to all)
- In a particular environment (M1 Mac, Ventura 13.4.1), we could not install it following the [existing documentation](https://pathvisio.org/downloads) (especially the Java 8 setup), so we hacked a way to install it in those environments and [posted an issue](https://github.com/PathVisio/pathvisio/issues/195) on [it's GitHub repository](https://github.com/PathVisio/pathvisio) so that it could be reflected. (ono)
- Create (or edit) and publish several pathway diagrams using PathVisio
- Representative anthocyanin biosynthetic pathway ([WP5391](https://www.wikipathways.org/pathways/WP5391.html)) (Bono)
- CBD synthetic pathway ([WP5392](https://www.wikipathways.org/pathways/WP5392.html)) (Oishi)
- Network map of SARS-CoV-2 signaling pathway ([WP5115](https://www.wikipathways.org/pathways/WP5115.html)) (Ono)

Future work:

- Spread the usage of WikiPathways, PathVisio & PFOCR so that more people can add and use more types and species of pathway data
- Make video tutorials (in TogoTV) on how to use, edit & add pathway data with WikiPathways, PathVisio, PFOCR. (ono)
- Standardize the method for curating pathway figures for each target species from the pfocr database, and render pathway diagrams for each target species based on the curated pathway figures.
- In the Python environment, py4cytoscape can be used to convert from DataFrame to Cytoscape format, but it is not possible to further convert from there to WikiPathways format. We believe that the ability to describe a GPML template from a generic description, such as tab-delimited text, would be an efficient pathway rendering method, and we will continue discussions on a conversion tool for this purpose.