Merge pull request #55 from omics-datascience/dev

Dev

.gitignore

@@ -145,8 +145,8 @@ src/api_service/experiments/venv
 docker-compose.yml
 /secretkey.txt
 /modulector/database_versions/
-modulector/files/EPIC-8v2-0_A1.csv
-modulector/files/mirDIP_Unidirectional_search_v.5.txt
+modulector/files/EPIC.csv
+modulector/files/mirDIP_Unidirectional_search.txt
 *.sql.gz
 modulector/files/tmp_db.csv
 docker-compose.mauri_dev.yml

DEPLOYING.md

@@ -134,28 +134,31 @@ You can use set Modulector DB in two ways.
 
 ### Regenerating the data manually
 
-1. Download the files for the mirDIP database (version 5.2) and the Illumina 'Infinium MethylationEPIC 2.0' array. The files can be freely downloaded from their respective web pages.  
+1. Download the files for the mirDIP database (version 5.2), Illumina 'Infinium MethylationEPIC 2.0' array and the Human MicroRNA Disease Database v4.0. The files can be freely downloaded from their respective web pages.  
    **For the mirDIP database**:
       - Go to the [MirDIP download web page](https://ophid.utoronto.ca/mirDIP/download.jsp) and download the file called *"mirDIPweb/mirDIP Unidirectional search ver. 5.2"*.
       - Unzip the file.
-      - Find the file called *"mirDIP_Unidirectional_search_v.5.txt"* and move it into the **"modulector/files/"** directory.  
+      - Find the file called *"mirDIP_Unidirectional_search.txt"* and move it into the **"modulector/files/"** directory.  
 
    **For the EPIC Methylation array**:
       - Go to the [Illumina product files web page](https://support.illumina.com/downloads/infinium-methylationepic-v2-0-product-files.html) and download the ZIP file called "*Infinium MethylationEPIC v2.0 Product Files (ZIP Format)*".
       - Unzip the file.
-      - Within the unzipped files you will find one called "*EPIC-8v2-0_A1.csv*". Move this file to the directory **"modulector/files/"**.
-      - **NOTE:** the total weight of both files is about 5 GB.
+      - Within the unzipped files you will find one called "*EPIC.csv*". Move this file to the directory **"modulector/files/"**.
+      - **NOTE:** the total weight of both files is about 5 GB.  
+
+    **For the HMDD database**:
+      - Go to the [HMDD website](https://www.cuilab.cn/hmdd) and from the *Downloads* tab, download the *txt* file from the option "The whole dataset of miRNA-disease association data". Use version 4.0.
+      - Rename the downloaded file as "*disease_hmdd.txt*". Move this file to the directory **"modulector/files/"**.  
 
    **For the mirBase database**: this database is embedded as it weighs only a few MBs. Its data is processed in Django migrations during the execution of the `python3 manage.py migrate` command. So, you don't have to do manual steps to incorporate mirBase data inside Modulector.
-1. Start up a PostgreSQL service. You can use the same service listed in the *docker-compose.dev.yml* file.
-1. Run `python3 manage.py migrate` to apply all the migrations (**NOTE:** this can take a long time to finish).
+2. Start up a PostgreSQL service. You can use the same service listed in the *docker-compose.dev.yml* file.
+3. Run `python3 manage.py migrate` to apply all the migrations (**NOTE:** this can take a long time to finish).
 
 ## Update databases
 
-Modulector currently works with the mirDIP (version 5.2) and miRBase (version 22.1) databases for miRNA data, and with information from the Illumina 'Infinium MethylationEPIC 2.0' array  for information about methylation sites.  
-If new versions are released for these databases, and you want to update them, follow these steps:  
+If new versions of the databases used in modulector are released and you want to update them, follow the following steps:  
 
-- For **mirDIP** and **Illumina EPIC array** you must follow the same steps described in the [Regenerating the data manually](#regenerating-the-data-manually) section, replacing the named files with the most recent versions that have been published on their sites .
+- For **mirDIP**, **HDMM** and **Illumina EPIC array** you must follow the same steps described in the [Regenerating the data manually](#regenerating-the-data-manually) section, replacing the named files with the most recent versions that have been published on their sites.
 - For **miRBase**, follow the instructions below:
    1. Go to the [*Download* section on the website][mirbase-download-page].
    1. Download the files named *hairpin.fa* and *mature.fa* from the latest version of the database.

ModulectorBackend/settings.py

@@ -13,7 +13,7 @@
 import os
 
 # Modulector version
-VERSION: str = '2.1.4'
+VERSION: str = '2.2.0'
 
 # Default primary key field type
 # https://docs.djangoproject.com/en/4.0/ref/settings/#default-auto-field

README.md

@@ -41,7 +41,7 @@ Modulector obtains information from different bioinformatics databases or resour
 2. miRNA data: [miRBase: the microRNA database](https://mirbase.org/).  
    miRBase is a searchable database of published miRNA sequences and annotations. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed hairpin in the database), with information on the location and sequence of the mature miRNA sequence (termed mature). Modulector use miRBase 22.1.  
 3. Relationship data between miRNA and diseases: [HMDD: the Human microRNA Disease Database](https://www.cuilab.cn/hmdd).  
-   Increasing reports have shown that miRNAs play important roles in various critical biological processes. For their importance, the dysfunctions of miRNAs are associated with a broad spectrum of diseases. The Human microRNA Disease Database (HMDD) is a database that curated experiment-supported evidence for human microRNA (miRNA) and disease associations. Modulector use HMDD v3.2 .
+   Increasing reports have shown that miRNAs play important roles in various critical biological processes. For their importance, the dysfunctions of miRNAs are associated with a broad spectrum of diseases. The Human microRNA Disease Database (HMDD) is a database that curated experiment-supported evidence for human microRNA (miRNA) and disease associations. Modulector use HMDD v4.0.
 4. Relationship data between miRNA and drugs: [SM2miR Database](http://www.jianglab.cn/SM2miR/).
    Many studies have demonstrated that bioactive small molecules (or drugs) can regulate the miRNA expression, which indicate that targeting miRNAs with small molecules is a new type of therapy for human diseases. SM2miR is a manual curated database which collects and incorporates the experimentally validated small molecules' effects on miRNA expression in 21 species from the published papers. Modulector uses leaked data from the SM2miR database for Homo Sapiens, in the version released on Apr. 27, 2015.
 5. Methylation data: Illumina [Infinium MethylationEPIC 2.0](https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html) array.  
@@ -551,21 +551,35 @@ This service provides information, with evidence supported by experiments, on th
     - `pubmed`: URL to the scientific article in the Pubmed database where the evidence that relates miRNA to the disease is found.
     - `description`: Short description of why this miRNA is related to this disease.
   - Example:
-    - URL: <http://localhost:8000/diseases/?mirna=hsa-miR-9500>
+    - URL: <http://localhost:8000/diseases/?mirna=hsa-miR-6511b>
     - Response:
 
       ```JSON
         {
-          "count":1,
+          "count":3,
           "next":null,
           "previous":null,
           "results":[
               {
-                  "id":3540992,
-                  "category":"target gene",
-                  "disease":"Liver Neoplasms",
-                  "pubmed":"https://pubmed.ncbi.nlm.nih.gov/24658401",
-                  "description":"The novel miR-9500 regulates the proliferation and migration of human lung cancer cells by targeting Akt1."
+                  "id": 4203307,
+                  "category": "other",
+                  "disease": "Lymphoma",
+                  "pubmed": "https://pubmed.ncbi.nlm.nih.gov/36248425",
+                  "description": "LncHOTAIR/hsa-miR-6511b-5p/ATG7 could regulate the proliferation, apoptosis, and autophagy of Raji and BJAB lymphoma cells."
+              },
+              {
+                  "id": 4207900,
+                  "category": "genetics_overexpression_promote",
+                  "disease": "Colorectal Neoplasms",
+                  "pubmed": "https://pubmed.ncbi.nlm.nih.gov/35590122",
+                  "description": "In vitro, overexpression of miR-6511b-5p inhibited metastasis by decreasing CD44 expression via directly targeting BRG1 in colorectal cancer."
+              },
+              {
+                  "id": 4241262,
+                  "category": "other",
+                  "disease": "gastric adenocarcinoma",
+                  "pubmed": "https://pubmed.ncbi.nlm.nih.gov/31772663",
+                  "description": "2) were recognized as prognostic and used for the construction of a STAD prognostic signature."
               }
           ]
         }

docker-compose_dist.yml

@@ -31,7 +31,7 @@ services:
 
     # Django Backend Server
     web_modulector:
-        image: omicsdatascience/modulector:2.1.4
+        image: omicsdatascience/modulector:2.2.0
         restart: always
         depends_on:
             - db_modulector