Merge pull request #717 from bigbio/dev

continue improvements to fix datasets.

Author: ypriverol

.github/workflows/validate-all.yml

@@ -52,6 +52,6 @@ jobs:
             python validate.py -v
           else
             export FILELIST=$HOME/filelist.txt
-            cat "$FILELIST" | while read line; do echo "Changed file: $line"; parse_sdrf validate-sdrf --sdrf_file $line --skip_factor_validation --skip_experimental_design_validation --use_ols_cache_only; done
+            cat "$FILELIST" | grep "*sdrf.tsv" | while read line; do echo "Changed file: $line"; parse_sdrf validate-sdrf --sdrf_file $line --skip_factor_validation --skip_experimental_design_validation --use_ols_cache_only; done
           fi
 

README.md

@@ -7,13 +7,12 @@
 ![Contributors](https://flat.badgen.net/github/contributors/bigbio/proteomics-metadata-standard)
 ![Watchers](https://flat.badgen.net/github/watchers/bigbio/proteomics-metadata-standard)
 ![Stars](https://flat.badgen.net/github/stars/bigbio/proteomics-metadata-standard)
-[![Read the Docs](https://readthedocs.org/projects/proteomics-sample-metadata/badge/?version=latest)](https://proteomics-sample-metadata.readthedocs.io/en/latest/)
 
 ## Improving metadata annotation of Proteomics datasets
 
 Metadata is essential in proteomics data repositories and is crucial to interpret and reanalyze the deposited data sets. While the dataset general description and standard data file formats are supported and captured for every dataset by ProteomeXchange partners, the information regarding the sample to data files is mostly missing. Recently, members of the European Bioinformatics Community for Mass Spectrometry (EuBIC - https://eubic-ms.org/) have created this open-source project to enable the standardization of sample metadata of public proteomics data sets.
 
-The Proteomics Sample Metadata Project aims to standardize the way ProteomeXchange partners and the proteomics community capture the relation between the _samples_ and the _data_ generated within a PX submission. We have adapted the [MAGE-TAB v1.1 format](https://www.fged.org/projects/mage-tab/) to capture necessary metadata for Proteomics experiments to allow automated re-processing. The MAGE-TAB (MicroArray Gene Expression Tabular) is the file format to store the metadata and sample information on transcriptomics experiments. By repurposing and extending the MAGE-TAB for Proteomics, we aim to provide a format for future submissions of multiomics experiments to ProteomeXchange partners and better integration with other omics data. The MAGE-TAB is divided in two main files: IDF (Investigation Description Format) and SDRF (Sample and Data Relationship Format). We will describe how these two files are adapted for Proteomics.
+The Proteomics Sample Metadata Project aims to standardize the way ProteomeXchange partners and the proteomics community capture the relation between the _samples_ and the _data_ generated within a PX submission. We have adapted the [MAGE-TAB v1.1 format](https://www.fged.org/projects/mage-tab/) to capture the necessary metadata for Proteomics experiments to allow automated re-processing. The MAGE-TAB (MicroArray Gene Expression Tabular) is the file format to store the metadata and sample information on transcriptomics experiments. By repurposing and extending the MAGE-TAB for Proteomics, we aim to provide a format for future submissions of multiomics experiments to ProteomeXchange partners and better integration with other omics data. The MAGE-TAB is divided in two main files: IDF (Investigation Description Format) and SDRF (Sample and Data Relationship Format). We will describe how these two files are adapted for Proteomics.
 
 Our goal is to ensure maximum reusability of the deposited data. Our work aims to define the minimum information required to report the experimental design of proteomics experiments, enabling the use and reuse of the deposited data by the proteomics community. The following _Use Cases_ should be considered to design the Proteomics Sample Metadata Format: