more updates to the paper, JOSS checklist

docs/paper.bib

@@ -76,4 +76,19 @@ @misc{topGO
   url = {https://bioconductor.org/packages/topGO}
 }
 
+@article{QuickGO,
+    author = {Binns, David and Dimmer, Emily and Huntley, Rachael and Barrell, Daniel and O'Donovan, Claire and Apweiler, Rolf},
+    title = "{QuickGO: a web-based tool for Gene Ontology searching}",
+    journal = {Bioinformatics},
+    volume = {25},
+    number = {22},
+    pages = {3045-3046},
+    year = {2009},
+    month = {09},
+    abstract = "{Summary: QuickGO is a web-based tool that allows easy browsing of the Gene Ontology (GO) and all associated electronic and manual GO annotations provided by the GO Consortium annotation groups QuickGO has been a popular GO browser for many years, but after a recent redevelopment it is now able to offer a greater range of facilities including bulk downloads of GO annotation data which can be extensively filtered by a range of different parameters and GO slim set generation.Availability and Implementation: QuickGO has implemented in JavaScript, Ajax and HTML, with all major browsers supported. It can be queried online at http://www.ebi.ac.uk/QuickGO. The software for QuickGO is freely available under the Apache 2 licence and can be downloaded from http://www.ebi.ac.uk/QuickGO/installation.htmlContact:  [email protected]; [email protected]}",
+    issn = {1367-4803},
+    doi = {10.1093/bioinformatics/btp536},
+    url = {https://doi.org/10.1093/bioinformatics/btp536},
+    eprint = {https://academic.oup.com/bioinformatics/article-pdf/25/22/3045/48997998/bioinformatics\_25\_22\_3045.pdf},
+}
 

docs/paper.md

@@ -37,7 +37,7 @@ The [Gene Ontology Consortium][GO] maintains GAF files for various organisms. Ty
 
 The most annotated gene in the human genome, `HTT1`, currently has 1098 annotations. Thus, even small lists of genes may have a large number of annotations presenting an extraordinary challenge for interpretation. There is a clear need to visualize shared gene functions in an informative manner. 
 
-Web-based tools designed to visualize gene ontology data include `AmiGO` [@AmiGO]. Command line tools like `goatools` [@goatools] support GO term lineage visualization. R packages like `topGO` [@topGO] implement GO structure visualizations of enriched GO terms. To our knowledge, no standalone software package specifically designed to filter and visualize gene ontology data derived from lists of genes exists at this time.
+Web-based tools designed to visualize and filter gene ontology data include `AmiGO` [@AmiGO] and `QuickGO` [@QuickGO]. Command line tools like `goatools` [@goatools] support GO term lineage visualization. R packages like `topGO` [@topGO] implement GO structure visualizations of enriched GO terms. We are unaware of locally installable software that specifically allows for interactive filtering and visualization of gene ontology derived on gene lists.
 
 GeneScape is a Python package that allows users to visualize a list of gene products in terms of the functional context represented by the Gene Ontology. GeneScape is distributed both as a command-line tool and as GUI-enabled standalone software that does not require Python to be installed on the user's computer, thus making it accessible to a wide range of users.