Online ressources
ODAM: Open Data for Access and Mining¶
(C) INRAE UMR 1332 BFP, PMB - 2020 - Version 1.1
We have grouped together here all the links to documents and software produced about ODAM, as well as those concerning the tools, specifications and repositories (data and software) used directly (production) or indirectly (use, referencing) by ODAM.
Online resources related to ODAM¶
| Description | Type | Link |
|---|---|---|
| Data Preparation Protocol for ODAM Compliance | Documentation | Data collection and preparation |
| API Documentation based on Swagger | Web API Tool | INRA-PMB/ODAM/1.2.0/ |
| R ODAM package and How to use it | Package | https://cran.r-project.org/package=Rodam |
| R ODAM package Vignette | Package | Rodam/vignettes/Rodam.html |
| Virtual Machine embedding the ODAM software on Oracle VM VirtualBox along with its installation guide | Virtual Machine + Documentation | https://doi.org/10.15454/C9LAEF |
| Docker containers on DockerHub for installing on a Linux machine | Container | https://hub.docker.com/r/odam/getdata/ https://hub.docker.com/r/odam/dataexplorer/ |
| A very lightweight local web server for Windows to deploy the ODAM API | Web API Tool | ODAMwebserver |
| Examples of Jupyter notebooks (R & Python) based on the ODAM Web API | Notebook | https://github.com/djacob65/binder_odam https://doi.org/10.24433/CO.8981049.v1 https://doi.org/10.24433/CO.0011270.v1 |
| Modeling the growth of tomato fruits based on enzyme activity profiles (Example of data analysis interfaced by ODAM) | Notebook | https://hal.inrae.fr/hal-02611223 |
| ODAM Source code on GitHub | Source Code | https://github.com/inrae/ODAM |
| ODAM Source code on Software Heritage | Source Code | https://www.softwareheritage.org/ |
| JSON Schema for ODAM data package | Source Code | https://github.com/djacob65/odam-datapackage/ |
Note : In order either to improve the use of ODAM or to complement its toolbox, a number of additional developments are planned.
External resources used¶
Tools
| Name | Description | Link |
|---|---|---|
| docker | Container management tool | https://www.docker.com/ |
| Oracle VM VirtualBox | Virtual Machine (VM) management tool | https://www.virtualbox.org/ |
| Rstudio | Integrated Development Environment (IDE) for R | https://rstudio.com/ |
| R shiny | interactive web apps for R | https://shiny.rstudio.com/ |
| jupyter notebook | Web application for e-notebooks | https://jupyter.org/ |
| q-text-as-data | A command line tool for running SQL directly on CSV or TSV files | http://harelba.github.io/q/ |
| sqlite3 | A command line tool for executing SQL statements against an SQLite database | https://www.sqlite.org/cli.html |
| goodtables.io | data publishing with confidence - data validation on every change | http://goodtables.io/ |
| codemeta-generator | Create your codemeta file | https://codemeta.github.io/codemeta-generator/ |
| ---- |
Repositories
| Name | Type | Link |
|---|---|---|
| GitHub | Source code | https://github.com/ |
| Software Heritage | Source Code | https://www.softwareheritage.org/ |
| Docker Hub | Containers | https://hub.docker.com/ |
| Data INRAE | Data | https://data.inrae.fr/ |
| HAL INRAE | Documents | https://hal.inrae.fr/ |
| protocols.io | Documents | https://www.protocols.io/ |
| Code Ocean | Notebooks | https://codeocean.com/ |
| R cran | Source code | https://cran.r-project.org/ |
Specifications
| Name | Type | Link |
|---|---|---|
| Swagger | API schema | https://swagger.io/specification/ |
| Data Packages | Data schema | https://specs.frictionlessdata.io/data-package/ |
| The CodeMeta Project | Code metadata schema | https://codemeta.github.io/ |
Registries
| Name | Type | Link |
|---|---|---|
| bio.tools | Tool and data services registry. | https://bio.tools/ |
| RRID | Research Resource Identification registry | https://scicrunch.org/browse/resourcedashboard |
| Identifiers | Central registry which provides compact identifiers | https://registry.identifiers.org/ |
| FAIRsharing | Standards, databases and policies registry | https://fairsharing.org/ |
| RDA Metadata Directory | Standards, extensions, tools, use cases | https://rd-alliance.github.io/metadata-directory/ |
FAIR evaluation/assessment grids
| Name | Link |
|---|---|
| 5 ★ Data Rating Tool | https://data.csiro.au/collection/csiro:27133 |
| RDA FAIR Data Maturity Model WG | https://www.rd-alliance.org/groups/fair-data-maturity-model-wg |
| RDA Sharing Rewards and Credit IG | https://www.rd-alliance.org/groups/sharing-rewards-and-credit-sharc-ig |
Tools used for this online documentation¶
| Name | Link |
|---|---|
| Make the Docs | https://www.mkdocs.org/ |
| Material for MkDocs | https://squidfunk.github.io/mkdocs-material/ |
| Lightbox | https://lokeshdhakar.com/projects/lightbox2/ |
| Mermaid | http://mermaid-js.github.io/mermaid/ |
