Merge pull request #4 from SwissOpenEM/update-WP3

updated WP content

_data/deliverables-wp/wp3.yml

@@ -4,5 +4,5 @@
   table: "tec"
 - id: 2
   description: "Expanding automated deposition tools for other EM disciplines"
-  status: "Open"
+  status: "In Progress"
   table: "tec"

assets/css/customOpenEM.scss

@@ -398,6 +398,7 @@ footer {
   color: white;
   font-weight: bold;
 
+
   &.open {
     background-color: #e74c3c;
     /* Rot */

deliverable-wp1.md

@@ -54,19 +54,19 @@ The Metadata Standards work package contains the following tasks and components.
 
 #### Metadata-Standards-1: Community consensus and commitment to data collection standards ####
 
-Established the <a href="https://github.com/osc-em">Open Standards Community for EM</a>
-Workshop 22-23 Feb 2024 with participants from facilities, software, and repositories
-Draft schema available for EM metadata. The goal is to include metadata required for future processing and deposition.
-Schema terms are defined by existing ontologies where available: CryoEM ontology, PDBx/mmCIF dictionary, Helmholz EM Glossary, NeXus-FAIRmat NXem format
-Conversion tools under development for major instrument manufacturers and formats
-Coordinate with PREMISE project regarding terms and ontologies
+- Established the <a href="https://github.com/osc-em">Open Standards Community for EM</a>
+- Workshop 22-23 Feb 2024 with participants from facilities, software developers and repository curators.
+- Schema is now <a href="https://osc-em.github.io/OSCEM_Schemas/">available</a> for EM metadata. During the next milestones, metadata required for processing will be included by our collaborators and support for Material Sciences will be extended. 
+- Schema terms are defined with respect to existing ontologies where available: CryoEM ontology, PDBx/mmCIF dictionary, Helmholtz EM Glossary, NeXus-FAIRmat NXem format.
+- Tools available for major instrument manufacturers and formats (Thermo Fisher EPU and SerialEM)
+- Ontologies are also coordinated with the PREMISE project 
 
 #### Metadata-Standards-2: Ensure streamlined and automatic metadata harvesting at all ETH sites ####
 
 Metadata extraction tools for life sciences <a href="https://github.com/SwissOpenEM/LS_Metadata_reader">(LS-Metadata Reader)</a> and material science <a href="https://github.com/SwissOpenEM/metadata-extractor">(Metadata-Extractor)</a>
 
 #### Metadata-Standards-3: SciCat Dataset Ingestor ####
 
-- <a href="https://github.com/paulscherrerinstitute/scicat-cli">SciCat CLI</a>
-- Web-based front-end planned
-- Fast data transfer using Globus
+- Fast data transfer using Globus (PSI) and S3 (ETHZ) to the archiver systems is available 
+- Web-based UI for data ingestion is supported by SciCat/ GUI application. Instrument metadata is automatically extracted while user enters sample metadata and authorship
+- <a href="https://github.com/paulscherrerinstitute/scicat-cli">SciCat CLI</a> was updated to a new version of SciCat backend

deliverable-wp3.md

@@ -53,11 +53,10 @@ The Deposition in International Repositories work package contains the following
 ### Tasks ### 
 
 #### Deposition-1: Developing automated deposition tools for cryo-EM ####
-
-Early access to wwPDB’s OneDep API, which provides a method for depositing life science datasets to EMDB and PDB.
-<a href="https://github.com/osc-em/converter-JSON-to-mmCIF">OSC-EM to mmCIF format converter</a> developed for metadata interoperability.
+To deposit biological specimen data, the European Bioinformatics Institute (EMBL-EBI) offers three central repositories relevant to Cryo-EM data. Early access to the testing version of OneDep API provides a method of depositing datasets to EMDB and PDB. <a href="https://github.com/osc-em/converter-OSCEM-to-mmCIF">OSCEM to mmCIF format converter</a> is developed for metadata interoperability between OSCEM and OneDep PDBx/mmCIF syntax. A Web-based UI on top of SciCat allows for the upload of processed files to create OneDep depositions. Additional functionality will be added to the <a href="https://github.com/SwissOpenEM/Depositor">depositor</a> to create depositions of raw datasets in EMPIAR.
 
 #### Deposition-2: Expanding automated deposition tools for other EM disciplines ####
-
-- Material Science support in OSC-EM
-- Exploring possible repositories (NOMAD, Material Science Cloud)
+Compared to task 1 of this deliverable, there are no central repositories as those offered by EBI. We are exploring possible repositories for depositions and considering the following projects:
+- The <a href="https://nomad-lab.eu/nomad-lab/">NOMAD project</a> lists data from EELS experiments and offers an API to interact with
+- <a href="https://www.materialscloud.org/home">Material Science Cloud</a> offers an archiving solution in any format and enables integration with other services, such as built-in visualizations and workflow managers.  
+During the next milestones, we will work on integrating deposition from SciCat to these repositories.