Added citation cff

Author: AlexJSully

CHANGELOG.md

@@ -10,26 +10,26 @@ To see tags and releases, please go to [Tags](https://github.com/BioAnalyticReso
 
 Optimization:
 
-- Addressed client-side caching for faster loading
-- Improved performance of mouse hover listeners
-- Optimized images
+-   Addressed client-side caching for faster loading
+-   Improved performance of mouse hover listeners
+-   Optimized images
 
 Update:
 
-- Added ESLint
-- No longer supporting Internet Explorer
-- Updated packages
+-   Added ESLint
+-   No longer supporting Internet Explorer
+-   Updated packages
 
 Documentation:
 
-- Fixed links in markdown files
-- Updated README's examples
+-   Fixed links in markdown files
+-   Updated README's examples
 
 Bug fix:
 
-- Fixed `localStorage` failing to initialize and store/call data
-- Fixed issue where cannot call `generateSVG`
-- Fixed issue with favicons, now uses BAR's favicon over local (same for web manifest)
+-   Fixed `localStorage` failing to initialize and store/call data
+-   Fixed issue where cannot call `generateSVG`
+-   Fixed issue with favicons, now uses BAR's favicon over local (same for web manifest)
 
 ## [1.0.19] - 2022-11-03
 

CITATION.cff

@@ -0,0 +1,78 @@
+cff-version: 1.2.0
+title: ePlant Plant eFP
+message: >-
+    A data visualization tool to display tissue expression data for Arabidopsis thaliana
+type: software
+authors:
+    - given-names: Alexander
+      family-names: Sullivan
+      email: alexjsully.connect@outlook.com
+      orcid: "https://orcid.org/0000-0002-4463-4473"
+    - given-names: Michael N
+      family-names: Lombardo
+    - given-names: Asher
+      family-names: Pasha
+      orcid: "https://orcid.org/0000-0002-9315-0520"
+    - given-names: Vincent
+      family-names: Lau
+    - given-names: Jian Yun
+      family-names: Zhuang
+    - given-names: Ashley
+      family-names: Christendat
+    - given-names: Bruno
+      family-names: Pereira
+    - given-names: Tianhui
+      family-names: Zhao
+    - given-names: Youyang
+      family-names: Li
+    - given-names: Rachel
+      family-names: Wong
+    - given-names: Faisal Z
+      family-names: Qureshi
+      affiliation: University of Ontario Institute of Technology
+    - given-names: Nicholas J.
+      family-names: Provart
+      orcid: "https://orcid.org/0000-0001-5551-7232"
+      email: nicholas.provart@utoronto.ca
+      affiliation: University of Toronto
+identifiers:
+    - type: doi
+      value: 10.1093/nar/gkae920
+repository-code: "https://github.com/BioAnalyticResource/ePlant_Plant_eFP"
+url: "https://bar.utoronto.ca/"
+abstract: >-
+    The Bio-Analytic Resource for Plant Biology ('the BAR', at
+    https://bar.utoronto.ca) is celebrating its 20th year in
+    operation in 2025. The BAR encompasses and provides
+    visualization tools for large 'omics data sets from
+    plants. The BAR covers data from Arabidopsis, tomato,
+    wheat, barley and 29 other plant species (with data for 2
+    others to be released soon). These data include nucleotide
+    and protein sequence data, gene expression data,
+    protein-protein and protein-DNA interactions, protein
+    structures, subcellular localizations, and polymorphisms.
+    The data are stored in more than 200 relational databases
+    holding 186 GB of data and are presented to the
+    researchers via web apps. These web apps provide data
+    analysis and visualization tools. Some of the most popular
+    tools are eFP ('electronic fluorescent pictograph')
+    Browsers, ePlants and ThaleMine (an Arabidopsis-specific
+    instance of InterMine). The BAR was designated a Global
+    Core Biodata Resource in 2023. Like other GCBRs, the BAR
+    has excellent operational stability, provides access
+    without login requirement, and provides an API for
+    researchers to be able to access BAR data
+    programmatically. We present in this update a new
+    overarching search tool called Gaia that permits easy
+    access to all BAR data, powered by machine learning and
+    artificial intelligence.
+keywords:
+    - agriculture
+    - bioinformatics
+    - computational biology
+    - data visualization
+    - NLP
+    - web application
+commit: a7056e48e4d90f48a053ab561be30f98ee5de7c4
+version: 1.0.20
+date-released: "2024-01-15"

README.md

@@ -2,6 +2,8 @@
 
 The ePlant Plant eFP is a tissue expression API provided by the [Bio-Analytic Resource for Plant Biology (BAR)](https://bar.utoronto.ca/) from the University of Toronto. This tool will provide visualized tissue expression data corresponding for Arabidopsis thaliana with one of the listed [compendiums](./compendiums).
 
+Official publication of the [ePlant Plant eFP](https://bar.utoronto.ca) can be found at <https://doi.org/10.1093/nar/gkae920> & <https://doi.org/10.1101/2021.04.28.441805>.
+
 [![Maintainability](https://api.codeclimate.com/v1/badges/ed34ffac71dd5a1b2d72/maintainability)](https://codeclimate.com/github/BioAnalyticResource/ePlant_Plant_eFP/maintainability)
 [![Follow on Twitter](https://img.shields.io/twitter/follow/BAR_PlantBio?style=social)](https://twitter.com/BAR_PlantBio)
 [![GitHub repo size](https://img.shields.io/github/repo-size/BioAnalyticResource/ePlant_Plant_eFP)](https://github.com/BioAnalyticResource/ePlant_Plant_eFP)

package-lock.json

@@ -3,7 +3,7 @@
 	"contributors": [
 		{
 			"name": "Alexander Sullivan",
-			"email": "alexander.j.sullivan@hotmail.com",
+			"email": "alexjsully.connect@outlook.com",
 			"url": "https://alexjsully.me/"
 		},
 		{
@@ -31,11 +31,12 @@
 	},
 	"main": "tissueExpressionBAR.js",
 	"scripts": {
-		"eslint": "eslint --fix ./ --ignore-path .prettierignore",
+		"audit:fix": "npm i && npm audit fix",
 		"eslint:check": "eslint ./ --ignore-path .prettierignore",
-		"pre-commit": "npm run prettier && npm run eslint",
+		"eslint": "eslint --fix ./ --ignore-path .prettierignore",
+		"prettier:check": "prettier --check ./",
 		"prettier": "prettier --write ./",
-		"prettier:check": "prettier --check ./"
+		"validate": "npm run prettier && npm run eslint"
 	},
 	"directories": {
 		"example": "example"