refactor (networks/symptom): symptom-disease organization refactoring

datasci4health · May 26, 2024 · f52e7e8 · f52e7e8
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diff --git a/networks/symptom-disease/README.md b/networks/symptom-disease/README.md
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 Goh, K. il, Cusick, M. E., Valle, D., Childs, B., Vidal, M., & Barabási, A. L. (2007). The human disease network. Proceedings of the National Academy of Sciences of the United States of America, 104(21), 8685–8690. https://doi.org/10.1073/PNAS.0701361104
 
-Zhou, X., Menche, J., Barabási, A.-L., & Sharma, A. (2014). Human symptoms–disease network. Nature Communications, 5(1), 4212. https://doi.org/10.1038/ncomms5212
+Zhou, X., Menche, J., Barabási, A.-L., & Sharma, A. (2014). Human symptoms–disease network. Nature Communications, 5(1), 4212. https://doi.org/10.1038/ncomms5212
+
+## Class 2024-04-30 Network Science - Mapping and Transforming
+
+* folder `mapping-transforming`
+
+Orange workflow `converte-list-rows.ows` prepares files of three sources:
+* `01-source-nature` - original from the articles on Nature
+* `02-source-human-phenotype-ontology` - Human Phenotype Ontology (genes x diseases)
+* `03-source-comparative-toxicogenomics-database` - Comparative Toxicogenomics Database (maps MeSH to OMIM)
+
+Prepared files are saved at:
+
+* `04-prepared` - files to be read and processed by Cypher
+
+## Class 2024-05-02 Mapping and Workflow
+
+* folder `mapping-transforming`
+
+Relations between symptoms and diseases manually selected and stored in:
+* `05-manually-selected` -  rationale stored at `symptom-disease(selected).xlsx`
+
+Besides processing the simple example in Cypher, there two equivalent examples:
+
+* `06-jupyter-networkx` - Jupyter example using NetworkX (files are also converted to Pajek for Orange)
+* `07-orange-network` - Orange example using networks 
+
+## Class 2024-05-09 Clusters and Communities
+
+* folder `cluster-module`
+
+* `01-preprocess` - data from symptoms and diseases are converted by Orange to a network disease-disease with different similarity thresholds (0.8 and 0.95)
+
+This data is source to the other three projects:
+
+* `02-cytoscape` - networks are imported to CytoScape, which infers communities
+* `03-jupyter-networkx` - networks are imported, displayed and converted (to Pajek for Orange) at Jupyter with NetworkX
+* `04-orange-cluster-network` - clusters and communities (network) are compared
diff --git a/...1467_2014_BFncomms5212_MOESM1046_ESM).tsv → ...1467_2014_BFncomms5212_MOESM1046_ESM).tsv b/...1467_2014_BFncomms5212_MOESM1046_ESM).tsv → ...1467_2014_BFncomms5212_MOESM1046_ESM).tsv
diff --git a/...1467_2014_BFncomms5212_MOESM1045_ESM).tsv → ...1467_2014_BFncomms5212_MOESM1045_ESM).tsv b/...1467_2014_BFncomms5212_MOESM1045_ESM).tsv → ...1467_2014_BFncomms5212_MOESM1045_ESM).tsv
diff --git a/...sease-disease-minimum-0.70-similarity.tab → ...sease-disease-minimum-0.70-similarity.tab b/...sease-disease-minimum-0.70-similarity.tab → ...sease-disease-minimum-0.70-similarity.tab
diff --git a/...sease-disease-minimum-0.80-similarity.tab → ...sease-disease-minimum-0.80-similarity.tab b/...sease-disease-minimum-0.80-similarity.tab → ...sease-disease-minimum-0.80-similarity.tab
diff --git a/...sease-disease-minimum-0.85-similarity.tab → ...sease-disease-minimum-0.85-similarity.tab b/...sease-disease-minimum-0.85-similarity.tab → ...sease-disease-minimum-0.85-similarity.tab
diff --git a/...e-minimum-0.95-similarity-selected-g1.csv → ...e-minimum-0.95-similarity-selected-g1.csv b/...e-minimum-0.95-similarity-selected-g1.csv → ...e-minimum-0.95-similarity-selected-g1.csv
diff --git a/...e-minimum-0.95-similarity-selected-g2.csv → ...e-minimum-0.95-similarity-selected-g2.csv b/...e-minimum-0.95-similarity-selected-g2.csv → ...e-minimum-0.95-similarity-selected-g2.csv
diff --git a/...e-minimum-0.95-similarity-selected-g3.csv → ...e-minimum-0.95-similarity-selected-g3.csv b/...e-minimum-0.95-similarity-selected-g3.csv → ...e-minimum-0.95-similarity-selected-g3.csv
diff --git a/...ease-minimum-0.95-similarity-selected.csv → ...ease-minimum-0.95-similarity-selected.csv b/...ease-minimum-0.95-similarity-selected.csv → ...ease-minimum-0.95-similarity-selected.csv
diff --git a/...sease-disease-minimum-0.95-similarity.tab → ...sease-disease-minimum-0.95-similarity.tab b/...sease-disease-minimum-0.95-similarity.tab → ...sease-disease-minimum-0.95-similarity.tab
diff --git a/...ter-module/selected-symptoms-diseases.csv → ...ter-module/selected-symptoms-diseases.csv b/...ter-module/selected-symptoms-diseases.csv → ...ter-module/selected-symptoms-diseases.csv
diff --git a/...cess/cluster-module/selected-symptoms.csv → ...rget-cluster-module/selected-symptoms.csv b/...cess/cluster-module/selected-symptoms.csv → ...rget-cluster-module/selected-symptoms.csv
diff --git a/...ster-module/preprocess/cluster-module.ows → ...r-module/01-preprocess/cluster-module.ows b/...ster-module/preprocess/cluster-module.ows → ...r-module/01-preprocess/cluster-module.ows
diff --git a/...-module/cytoscape/cluster-module-0.75.cys → ...dule/02-cytoscape/cluster-module-0.75.cys b/...-module/cytoscape/cluster-module-0.75.cys → ...dule/02-cytoscape/cluster-module-0.75.cys
diff --git a/...-module/cytoscape/cluster-module-0.80.cys → ...dule/02-cytoscape/cluster-module-0.80.cys b/...-module/cytoscape/cluster-module-0.80.cys → ...dule/02-cytoscape/cluster-module-0.80.cys
diff --git a/...le/cytoscape/cluster-module-selection.cys → ...02-cytoscape/cluster-module-selection.cys b/...le/cytoscape/cluster-module-selection.cys → ...02-cytoscape/cluster-module-selection.cys
diff --git a/...ase-disease-minimum-0.80-similarity.ipynb → ...ase-disease-minimum-0.80-similarity.ipynb b/...ase-disease-minimum-0.80-similarity.ipynb → ...ase-disease-minimum-0.80-similarity.ipynb
diff --git a/...sease-disease-minimum-0.80-similarity.net → ...sease-disease-minimum-0.80-similarity.net b/...sease-disease-minimum-0.80-similarity.net → ...sease-disease-minimum-0.80-similarity.net
diff --git a/...sease-disease-minimum-0.80-similarity.tab → ...sease-disease-minimum-0.80-similarity.tab b/...sease-disease-minimum-0.80-similarity.tab → ...sease-disease-minimum-0.80-similarity.tab
diff --git a/...selected-diseases-diseases-similarity.csv → ...selected-diseases-diseases-similarity.csv b/...selected-diseases-diseases-similarity.csv → ...selected-diseases-diseases-similarity.csv
diff --git a/...lected-diseases-diseases-simularity.ipynb → ...lected-diseases-diseases-similarity.ipynb b/...lected-diseases-diseases-simularity.ipynb → ...lected-diseases-diseases-similarity.ipynb
diff --git a/...selected-diseases-diseases-similarity.net → ...selected-diseases-diseases-similarity.net b/...selected-diseases-diseases-similarity.net → ...selected-diseases-diseases-similarity.net
diff --git a/...module/orange/cluster-module-selected.ows → ...uster-network/cluster-module-selected.ows b/...module/orange/cluster-module-selected.ows → ...uster-network/cluster-module-selected.ows
diff --git a/...sease-disease-minimum-0.80-similarity.net → ...sease-disease-minimum-0.80-similarity.net b/...sease-disease-minimum-0.80-similarity.net → ...sease-disease-minimum-0.80-similarity.net
diff --git a/...selected-diseases-diseases-similarity.csv → ...selected-diseases-diseases-similarity.csv b/...selected-diseases-diseases-similarity.csv → ...selected-diseases-diseases-similarity.csv
diff --git a/...selected-diseases-diseases-similarity.net → ...selected-diseases-diseases-similarity.net b/...selected-diseases-diseases-similarity.net → ...selected-diseases-diseases-similarity.net
diff --git a/.../orange/selected-symptoms-vs-diseases.csv → ...network/selected-symptoms-vs-diseases.csv b/.../orange/selected-symptoms-vs-diseases.csv → ...network/selected-symptoms-vs-diseases.csv
diff --git a/...-transforming/01-source-nature/disease-disease(41467_2014_BFncomms5212_MOESM1046_ESM).tsv b/...-transforming/01-source-nature/disease-disease(41467_2014_BFncomms5212_MOESM1046_ESM).tsv
diff --git a/...1467_2014_BFncomms5212_MOESM1043_ESM).tsv → ...1467_2014_BFncomms5212_MOESM1043_ESM).tsv b/...1467_2014_BFncomms5212_MOESM1043_ESM).tsv → ...1467_2014_BFncomms5212_MOESM1043_ESM).tsv
diff --git a/...-transforming/01-source-nature/symptom-disease(41467_2014_BFncomms5212_MOESM1045_ESM).tsv b/...-transforming/01-source-nature/symptom-disease(41467_2014_BFncomms5212_MOESM1045_ESM).tsv
diff --git a/...1467_2014_BFncomms5212_MOESM1044_ESM).tsv → ...1467_2014_BFncomms5212_MOESM1044_ESM).tsv b/...1467_2014_BFncomms5212_MOESM1044_ESM).tsv → ...1467_2014_BFncomms5212_MOESM1044_ESM).tsv
diff --git a/...type-ontology/diseases_for_HP_0001909.csv → ...type-ontology/diseases_for_HP_0001909.csv b/...type-ontology/diseases_for_HP_0001909.csv → ...type-ontology/diseases_for_HP_0001909.csv
diff --git a/...ype-ontology/diseases_for_HP_0001909.xlsx → ...ype-ontology/diseases_for_HP_0001909.xlsx b/...ype-ontology/diseases_for_HP_0001909.xlsx → ...ype-ontology/diseases_for_HP_0001909.xlsx
diff --git a/...enotype-ontology/genes_for_HP_0001909.csv → ...enotype-ontology/genes_for_HP_0001909.csv b/...enotype-ontology/genes_for_HP_0001909.csv → ...enotype-ontology/genes_for_HP_0001909.csv
diff --git a/...notype-ontology/genes_for_HP_0001909.xlsx → ...notype-ontology/genes_for_HP_0001909.xlsx b/...notype-ontology/genes_for_HP_0001909.xlsx → ...notype-ontology/genes_for_HP_0001909.xlsx
diff --git a/...omics-database/CTD_diseases(original).csv → ...omics-database/CTD_diseases(original).csv b/...omics-database/CTD_diseases(original).csv → ...omics-database/CTD_diseases(original).csv
diff --git a/...-toxicogenomics-database/CTD_diseases.csv → ...-toxicogenomics-database/CTD_diseases.csv b/...-toxicogenomics-database/CTD_diseases.csv → ...-toxicogenomics-database/CTD_diseases.csv
diff --git a/...symptom-disease/prepared/disease-gene.csv → ...transforming/04-prepared/disease-gene.csv b/...symptom-disease/prepared/disease-gene.csv → ...transforming/04-prepared/disease-gene.csv
diff --git a/...ptom-disease/prepared/disease-symptom.csv → ...nsforming/04-prepared/disease-symptom.csv b/...ptom-disease/prepared/disease-symptom.csv → ...nsforming/04-prepared/disease-symptom.csv
diff --git a/...rks/symptom-disease/prepared/diseases.csv → ...ing-transforming/04-prepared/diseases.csv b/...rks/symptom-disease/prepared/diseases.csv → ...ing-transforming/04-prepared/diseases.csv
diff --git a/networks/symptom-disease/prepared/genes.csv → ...apping-transforming/04-prepared/genes.csv b/networks/symptom-disease/prepared/genes.csv → ...apping-transforming/04-prepared/genes.csv
diff --git a/...rks/symptom-disease/prepared/symptoms.csv → ...ing-transforming/04-prepared/symptoms.csv b/...rks/symptom-disease/prepared/symptoms.csv → ...ing-transforming/04-prepared/symptoms.csv
diff --git a/...ase/nature/symptom-disease(selected).xlsx → ...y-selected/symptom-disease(selected).xlsx b/...ase/nature/symptom-disease(selected).xlsx → ...y-selected/symptom-disease(selected).xlsx
diff --git a/...rkx/symptom-disease-edges_simple-case.csv → ...ted/symptom-disease-edges_simple-case.csv b/...rkx/symptom-disease-edges_simple-case.csv → ...ted/symptom-disease-edges_simple-case.csv
diff --git a/...rkx/symptom-disease-nodes_simple-case.csv → ...ted/symptom-disease-nodes_simple-case.csv b/...rkx/symptom-disease-nodes_simple-case.csv → ...ted/symptom-disease-nodes_simple-case.csv
diff --git a/...-networkx/analysing-symptom-disease.ipynb → ...-networkx/analysing-symptom-disease.ipynb b/...-networkx/analysing-symptom-disease.ipynb → ...-networkx/analysing-symptom-disease.ipynb
diff --git a/...ure/symptom-disease-edges_simple-case.csv → ...rkx/symptom-disease-edges_simple-case.csv b/...ure/symptom-disease-edges_simple-case.csv → ...rkx/symptom-disease-edges_simple-case.csv
diff --git a/...rkx/symptom-disease-edges_simple-case.net → ...rkx/symptom-disease-edges_simple-case.net b/...rkx/symptom-disease-edges_simple-case.net → ...rkx/symptom-disease-edges_simple-case.net
diff --git a/...ure/symptom-disease-nodes_simple-case.csv → ...rkx/symptom-disease-nodes_simple-case.csv b/...ure/symptom-disease-nodes_simple-case.csv → ...rkx/symptom-disease-nodes_simple-case.csv
diff --git a/...se/orange/simptom-disease_simple-case.ows → ...e-network/simptom-disease_simple-case.ows b/...se/orange/simptom-disease_simple-case.ows → ...e-network/simptom-disease_simple-case.ows
diff --git a/...nge/symptom-disease-edges_simple-case.net → ...ork/symptom-disease-edges_simple-case.net b/...nge/symptom-disease-edges_simple-case.net → ...ork/symptom-disease-edges_simple-case.net
diff --git a/...nge/symptom-disease-nodes_simple-case.csv → ...ork/symptom-disease-nodes_simple-case.csv b/...nge/symptom-disease-nodes_simple-case.csv → ...ork/symptom-disease-nodes_simple-case.csv
diff --git a/...ks/symptom-disease/convert-lista-rows.ows → ...apping-transforming/convert-list-rows.ows b/...ks/symptom-disease/convert-lista-rows.ows → ...apping-transforming/convert-list-rows.ows
diff --git a/networks/symptom-disease/cypher.md → ...om-disease/mapping-transforming/cypher.md b/networks/symptom-disease/cypher.md → ...om-disease/mapping-transforming/cypher.md
diff --git a/networks/symptom-disease/sub-networks.ows b/networks/symptom-disease/sub-networks.ows