Start JOSS paper. [skip ci]

.Rbuildignore

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 ^LICENSE\.md$
 ^README\.Rmd$
 ^\.github$
+paper.md
+paper.bib

.github/workflows/draft-pdf.yml

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+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: joss/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: joss/paper.pdf

joss/paper.bib

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+@article{RN13,
+   author = {Edera, Alejandro A and Milone, Diego H and Stegmayer, Georgina},
+   title = {Anc2vec: embedding gene ontology terms by preserving ancestors relationships},
+   journal = {Briefings in Bioinformatics},
+   volume = {23},
+   number = {2},
+   abstract = {The gene ontology (GO) provides a hierarchical structure with a controlled vocabulary composed of terms describing functions and localization of gene products. Recent works propose vector representations, also known as embeddings, of GO terms that capture meaningful information about them. Significant performance improvements have been observed when these representations are used on diverse downstream tasks, such as the measurement of semantic similarity between GO terms and functional similarity between proteins. Despite the success shown by these approaches, existing embeddings of GO terms still fail to capture crucial structural features of the GO. Here, we present anc2vec, a novel protocol based on neural networks for constructing vector representations of GO terms by preserving three important ontological features: its ontological uniqueness, ancestors hierarchy and sub-ontology membership. The advantages of using anc2vec are demonstrated by systematic experiments on diverse tasks: visualization, sub-ontology prediction, inference of structurally related terms, retrieval of terms from aggregated embeddings, and prediction of protein–protein interactions. In these tasks, experimental results show that the performance of anc2vec representations is better than those of recent approaches. This demonstrates that higher performances on diverse tasks can be achieved by embeddings when the structure of the GO is better represented. Full source code and data are available at https://github.com/sinc-lab/anc2vec.},
+   ISSN = {1477-4054},
+   DOI = {10.1093/bib/bbac003},
+   url = {https://doi.org/10.1093/bib/bbac003},
+   year = {2022},
+   type = {Journal Article}
+}
+
+@article{RN78,
+   author = {Nguyen, Jennifer H. and Curtis, Melissa A. and Imami, Ali S. and Ryan, William G. and Alganem, Khaled and Neifer, Kari L. and Nawor, Charlotte N. and Kistler, Brian P. and Miller, Gary W. and Shukla, Rammohan and McCullumsmith, Robert E. and Burkett, James P.},
+   title = {Developmental pyrethroid exposure disrupts molecular pathways for circadian rhythms and synaptic plasticity in mouse brain},
+   journal = {bioRxiv},
+   pages = {2023.08.28.555113},
+   abstract = {Neurodevelopmental disorders (NDDs) are a category of pervasive disorders of the developing nervous system with few or no recognized biomarkers. A significant portion of the risk for NDDs, including attention deficit hyperactivity disorder (ADHD), is contributed by the environment, and exposure to pyrethroid pesticides during pregnancy has been identified as a potential risk factor for NDD in the unborn child. We recently showed that low-dose developmental exposure to the pyrethroid pesticide deltamethrin in mice causes male-biased changes to ADHD- and NDD-relevant behaviors as well as the striatal dopamine system. Here, we used a multiomics approach to determine the broadest possible set of pharmacologically relevant changes in the mouse brain caused by developmental pyrethroid exposure (DPE). Using a litter-based, split-sample design, we exposed mouse dams during pregnancy and lactation to deltamethrin (3 mg/kg or vehicle every 3 days) at a concentration well below the EPA-determined benchmark dose used for regulatory guidance. We raised male offspring to adulthood, euthanized them, and pulverized and divided whole brain samples for split-sample transcriptomics, kinomics and multiomics integration. Transcriptome analysis revealed alterations to multiple canonical clock genes, and kinome analysis revealed changes in the activity of multiple kinases involved in synaptic plasticity. Multiomics integration revealed a dysregulated protein-protein interaction network containing primary clusters for mitogen-activated protein (MAP) kinase cascades, synaptic function, and the regulation of apoptosis. These results demonstrate that DPE causes a multi-modal biophenotype in the brain relevant to ADHD and identifies new potential avenues for therapeutics.Competing Interest StatementThe authors have declared no competing interest.},
+   DOI = {10.1101/2023.08.28.555113},
+   url = {https://www.biorxiv.org/content/biorxiv/early/2023/09/01/2023.08.28.555113.full.pdf},
+   year = {2023},
+   type = {Journal Article}
+}

joss/paper.md

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+---
+title: 'PAVER: Pathway Analysis Visualization with Embedding Representations'
+tags:
+- R
+- bioinformatics
+- pathway analysis
+date: "3 September 2023"
+output: pdf_document
+authors:
+- name: "William George Ryan V"
+  orcid: "0000-0003-4868-4002"
+  corresponding: yes
+  affiliation: 1
+bibliography: paper.bib
+affiliations:
+- name: The University of Toledo College of Medicine and Life Sciences Department of Neurosciences, USA
+  index: 1
+---
+
+# Summary
+
+PAVER is...
+
+# Statement of need
+
+We need PAVER because...
+
+# Acknowledgements
+
+We acknowledge...
+
+# References

renv.lock

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