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Merge pull request #44 from saezlab/41-expand-data-utilities
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41 expand data utilities
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vicpaton authored Jul 30, 2024
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14 changes: 14 additions & 0 deletions docs/src/api.rst
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data.network.get_omnipath
data.network.get_lianaplus
data.network.get_phosphositeplus
data.network.get_cosmos_pkn


Datasets
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data.omics.cptac_datatypes
data.omics.cptac_extend_dataframe

NCI60
~~~~~
.. module::networkcommons.data.omics
.. currentmodule:: networkcommons

.. autosummary::
:toctree: api
:recursive:

data.omics.nci60_datasets
data.omics.nci60_datatypes
data.omics.nci60_table


Other
~~~~~~~~
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7 changes: 7 additions & 0 deletions docs/src/contents.rst
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api


.. toctree::
:maxdepth: 2
:caption: Contribution guidelines

guidelines/guide_1_data


.. toctree::
:maxdepth: 2
:caption: Vignettes
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290 changes: 290 additions & 0 deletions docs/src/guidelines/guide_1_data.ipynb
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"source": [
"# Contribution's guideline: Data"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Thank you very much for considering contributing to the data collection of **NetworkCommons**! In order to make the resource as user-friendly as possible, we aim to be as transparent as possible, which means that all contributions should contain at least the following elements.\n",
"\n",
"## 1. Data information\n",
"* Experimental design: number of samples, number of experiments (if applicable), confounding factors\n",
"* Data production and processing: tools used, how the data processing was performed (if applicable).\n",
"* Files: number and type of files, with a small description of their contents.\n",
"* Link to the database from which the data was retrieved.\n",
"* Link to the dataset publication\n",
"* Path information explaining the structure of the data directories\n",
"This information should be appended to the existing YAML file in `networkcommons/data/datasets.yaml`\n",
"\n",
"An example of this can be found below:"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
".. code-block:: yaml\n",
"\n",
" NCI60:\n",
" name: NCI60\n",
" description: NCI-60 cell line data\n",
" publication_link: https://doi.org/10.1038/nrc1951\n",
" detailed_description: >-\n",
" This dataset contains data from the NCI-60 cell line panel.\n",
" It includes three files: TF activities from transcriptomics data,\n",
" metabolite abundances and gene reads.\n",
" path: NCI60/{cell_line}/{cell_line}__{data_type}.tsv"
]
},
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"source": [
"This information can then be accessed via `nc.data.omics.datasets()`"
]
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" <th>name</th>\n",
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" <th>publication_link</th>\n",
" <th>detailed_description</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>decryptm</th>\n",
" <td>DecryptM</td>\n",
" <td>Drug perturbation proteomics and phosphoproteomics data</td>\n",
" <td>https://doi.org/10.1126/science.ade3925</td>\n",
" <td>This dataset contains the profiling of 31 cancer drugs in 13 human cancer cell line models resulted in 1.8 million dose-response curves, including 47,502 regulated phosphopeptides, 7316 ubiquitinylated peptides, and 546 regulated acetylated peptides.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>panacea</th>\n",
" <td>Panacea</td>\n",
" <td>Pancancer Analysis of Chemical Entity Activity RNA-Seq data</td>\n",
" <td>https://doi.org/10.1016/j.xcrm.2021.100492</td>\n",
" <td>PANACEA contains dose-response and perturbational profiles for 32 kinase inhibitors in 11 cancer cell lines, in addition to a DMSO control. Originally, this resource served as the basis for a DREAM Challenge assessing the accuracy and sensitivity of computational algorithms for de novo drug polypharmacology predictions.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>moon</th>\n",
" <td>MOON</td>\n",
" <td>Database files for running MOON</td>\n",
" <td>https://example.com/moon</td>\n",
" <td>This dataset contains database files required for running the MOON software.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>cosmos</th>\n",
" <td>COSMOS</td>\n",
" <td>Database files for running COSMOS (MetaPKN)</td>\n",
" <td>https://example.com/cosmos</td>\n",
" <td>This dataset includes database files for the COSMOS software (MetaPKN).</td>\n",
" </tr>\n",
" <tr>\n",
" <th>CPTAC</th>\n",
" <td>CPTAC</td>\n",
" <td>Clinical Proteomic Tumor Analysis Consortium data</td>\n",
" <td>https://example.com/CPTAC</td>\n",
" <td>This dataset contains data from the Clinical Proteomic Tumor Analysis Consortium. It includes various cancer types and proteomic data.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>NCI60</th>\n",
" <td>NCI60</td>\n",
" <td>NCI-60 cell line data</td>\n",
" <td>https://example.com/NCI60</td>\n",
" <td>This dataset contains data from the NCI-60 cell line panel. It includes three files: TF activities from transcriptomics data, metabolite abundances and gene reads.</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
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"text/plain": [
" name \\\n",
"decryptm DecryptM \n",
"panacea Panacea \n",
"moon MOON \n",
"cosmos COSMOS \n",
"CPTAC CPTAC \n",
"NCI60 NCI60 \n",
"\n",
" description \\\n",
"decryptm Drug perturbation proteomics and phosphoproteomics data \n",
"panacea Pancancer Analysis of Chemical Entity Activity RNA-Seq data \n",
"moon Database files for running MOON \n",
"cosmos Database files for running COSMOS (MetaPKN) \n",
"CPTAC Clinical Proteomic Tumor Analysis Consortium data \n",
"NCI60 NCI-60 cell line data \n",
"\n",
" publication_link \\\n",
"decryptm https://doi.org/10.1126/science.ade3925 \n",
"panacea https://doi.org/10.1016/j.xcrm.2021.100492 \n",
"moon https://example.com/moon \n",
"cosmos https://example.com/cosmos \n",
"CPTAC https://example.com/CPTAC \n",
"NCI60 https://example.com/NCI60 \n",
"\n",
" detailed_description \n",
"decryptm This dataset contains the profiling of 31 cancer drugs in 13 human cancer cell line models resulted in 1.8 million dose-response curves, including 47,502 regulated phosphopeptides, 7316 ubiquitinylated peptides, and 546 regulated acetylated peptides. \n",
"panacea PANACEA contains dose-response and perturbational profiles for 32 kinase inhibitors in 11 cancer cell lines, in addition to a DMSO control. Originally, this resource served as the basis for a DREAM Challenge assessing the accuracy and sensitivity of computational algorithms for de novo drug polypharmacology predictions. \n",
"moon This dataset contains database files required for running the MOON software. \n",
"cosmos This dataset includes database files for the COSMOS software (MetaPKN). \n",
"CPTAC This dataset contains data from the Clinical Proteomic Tumor Analysis Consortium. It includes various cancer types and proteomic data. \n",
"NCI60 This dataset contains data from the NCI-60 cell line panel. It includes three files: TF activities from transcriptomics data, metabolite abundances and gene reads. "
]
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"## 2. Data handlers (API)\n",
"The data will either be deposited in the [NetworkCommons server](https://commons.omnipathdb.org/), or can be directly accessed from the original source. Regardless of this, the following functions are required\n",
"\n",
"* A function providing an overview of the subsets (if applicable). For example, check `nc.data.omics.decryptm_experiments()`. \n",
"* In case the data contains different files (for example, different omics layers, metadata tables, etc.), a function should retrieve this information. For example, check `nc.data.omics.nci60_datatypes()`\n",
"* A function that retrieves the data. For example, check `nc.data.omics.nci60_table()`. Ideally, a `pd.DataFrame`, but we are planning to expand support for `AnnData` instances.\n",
"\n",
"These new functions can be implemented in a new file, `_{dataset}`, inside the `networkcommons/data/omics/` folder.\n",
"\n",
"For example, `nc.data.omics.nci60_table()` retrieves a single `pd.DataFrame` by providing a data type and a cell line."
]
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" ID score\n",
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"1 NOC2L -1.480194\n",
"2 HES4 -0.781522\n",
"3 ISG15 0.406806\n",
"4 AGRN -0.324970"
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"nc.data.omics.nci60_table(cell_line='A498', data_type='RNA').head()"
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