Merge branch 'master' of github.com:BackofenLab/AxoWise into workAnlisha

backend/src/main.py

@@ -186,6 +186,16 @@ def chatbot_response():
     return Response(response, mimetype="application/json")
 
 
+# ====================== AI enrich text ======================
+# TODO Refactor this
+# Request comes from ContextSection.vue
+@app.route("/api/subgraph/textenrich", methods=["POST"])
+def enrich_text():
+    content = request.form.get("content")
+
+    return Response(json.dumps(content), mimetype="application/json")
+
+
 # ====================== Subgraph API ======================
 # request comes from home.js
 # TODO Refactor this

docs/journalStructure.md

@@ -23,20 +23,47 @@ This document contains the structure of Journals having Impact Factor greater th
 * ProteomeXchange Consortium - PeptideAtlas: stores datasets focusing on peptide identifications and their associated spectral evidence
 * ImmPort (Immunology Database and Analysis Portal)
 * Zenodo
+* China National GeneBank DataBase (CNGBdb)
+* BioProject
 
 
 _________________________________________________________________
 
 ## Cell: IF 45.5
-### Resource availability
-* materials availability
-* **Data and Code/Software Availability**
+_Structure 01:_
+### Resource availability:
+#### Materials availability
+#### Data and Code/Software Availability
+  * contains info regarding sequencing data and source code
   * if code unavailable > “This paper does not report original code” (MUST BE ADDED but not always added)
   * code available upon request from authors
   * already-existing SWs and Algorithms used but no unique code generated - found in Key Resources Table
   * ‘original code’
   * ‘unique code’
   * ‘custom code’
+  * github link for original source code or custom code generated by using already-existing SW
+
+_Structure 02:_
+### Data and Code/Software Availability:
+  * contains info regarding sequencing data and source code
+
+## Cell Stem Cell: IF 19.8 
+(some publications are not publicly accessible)
+### Resource availability:
+#### Lead contact
+  * requests for resources and reagents
+#### Materials availability 
+#### Data and Code/Software Availability
+  * section not found in several publications
+  * sequencing data listed but not source code
+  * 'original code'
+  * 'novel code'
+  * accession numbers of sequencing data & source code URL (Github/Zenodo) listed in Key Resources Table
+  * accession number stated in plain text instead of a URL
+
+## Other Cell journals:
+* Cancer Cell: 48.8
+* Immunity: 43.47
 
 ## Nature Immunology: IF 27.7
 ### Data availability
@@ -53,3 +80,20 @@ _________________________________________________________________
   * not provided
   * available from authors upon request
   * no new code, used existing code
+
+## Other Nature journals:
+* Nature Biotechnology: 68.2
+* Nature Medicine: 87.5
+* Nature Genetics: 31.7
+* Nature: 50.5
+* Nature Cell Biology: 17.3
+* Nature Neuroscience: 29.9
+* Nature Cancer: 38.7
+* Nature Methods: 36.1
+* Nature Metabolism: 25.5
+* Nature Protocols: 17.1
+* Nature Biomedical Engineering: 28.9
+* Nature Microbiology: 20.5
+
+
+Note: Most of the Science journals cannot be accessed without Institution registration.

frontend/package.json

@@ -18,9 +18,12 @@
     "d3": "^7.9.0",
     "d3-scale": "^4.0.2",
     "material-icons": "^1.13.12",
+    "file-saver": "^2.0.5",
     "mitt": "^3.0.1",
     "ml-hclust": "^3.1.0",
     "nouislider": "^15.8.1",
+    "quill": "^2.0.2",
+    "quill-to-word": "^1.3.0",
     "primeicons": "^7.0.0",
     "primevue": "^4.1.1",
     "random-color-rgb": "^1.1.1",

frontend/src/App.vue

@@ -1,5 +1,6 @@
 <template>
   <PersistentWindow />
+  <DocumentWindow />
   <router-view v-slot="{ Component }">
     <keep-alive exclude="HomeView">
       <component :is="Component" />
@@ -13,6 +14,7 @@ import CitationView from "@/views/CitationView.vue";
 import ProteinView from "@/views/ProteinView.vue";
 import HomeView from "@/views/HomeView.vue";
 import PersistentWindow from "@/components/PersistentWindow.vue";
+import DocumentWindow from "@/components/DocumentWindow.vue";
 
 export default {
   name: "App",
@@ -22,6 +24,7 @@ export default {
     HomeView,
     CitationView,
     PersistentWindow,
+    DocumentWindow,
   },
 };
 </script>