[{"_1":2,"_175":-5,"_176":-5},"loaderData",{"_3":4,"_13":14,"_21":22,"_154":155},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","routes/_layout",{"_15":-5,"_16":17,"_18":17,"_19":11,"_20":17},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","showHoneypotTrap","routes/_layout.r.$namespace.$reponame",{"_23":24,"_25":-5,"_26":11,"_27":11,"_28":29,"_30":31,"_32":-5,"_33":11,"_34":35,"_84":85,"_107":108,"_145":-5,"_146":11,"_147":17,"_148":11,"_149":-5,"_150":11,"_151":-5,"_152":153},"canonicalUrl","https://hub.docker.com/r/incertaesedis/cavatica/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","incertaesedis","reponame","cavatica","cloudBuildSource","isAutobuildsAvailable","repo",{"_36":37,"_38":39,"_41":42,"_43":44,"_45":11,"_46":47,"_48":49,"_50":51,"_53":31,"_28":29,"_54":55,"_56":40,"_57":58,"_59":58,"_60":61,"_62":-5,"_63":64,"_65":66,"_67":11,"_68":29,"_69":70,"_75":17,"_76":77,"_81":29,"_82":83},"categories",[],"content_types",[40],"image","date_registered","2018-08-07T21:57:47.018222Z","description","suite of pubmed and pmc textmining scripts","is_private","last_updated","2019-09-23T00:48:25.182718Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[52],"application/vnd.docker.container.image.v1+json","name","pull_count",290,"repository_type","star_count",1,"status","status_description","active","source","collaborator_count",0,"full_description","[![Build Status](https://travis-ci.org/incertae-sedis/cavatica.svg?branch=master)](https://travis-ci.org/incertae-sedis/cavatica) [![github release](https://img.shields.io/github/release/incertae-sedis/cavatica.svg?label=current+release)](https://github.com/incertae-sedis/cavatica/releases) [![https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg](https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg)](https://singularity-hub.org/collections/1322) [![Docker Automated build](https://img.shields.io/docker/cloud/build/incertaesedis/cavatica.svg)](https://hub.docker.com/r/incertaesedis/cavatica/) [![Docker Pulls](https://img.shields.io/docker/pulls/incertaesedis/cavatica.svg)](https://hub.docker.com/r/incertaesedis/cavatica/)\n\n**Initial Commit**: July 2016 \n

***** Cavatica has been adopted by the incertae-sedis group. *****

\n\n# Cavatica\nCode and pipeline for fetching PubMed and PubMed Central data and co-author network analysis. This tool can be used to identify author trends among several search terms. \n\nAn example, I've used these scripts to do a multi-network analysis of network analysis papers and their software. \n[Wiki Page Here](https://github.com/incertae-sedis/cavatica/wiki)\n\n $\"Added\"$ \n\nThe name comes from Charlotte's Web since her full name was Charlotte A. Cavatica. Although Cavatica also refers to barn spider.\n\n## Pipeline\n\n

***** Cavatica pipeline has been modified so no longer relies on Ebot. *****

\n\n $\"Plan\"$ \n\n\n\n## Dependencies\n\n* Some type of Linux Terminal where you can run Bash. (Cygwin if you're on Windows. Terminal already preinstalled on Mac)\n* R (check if installed by typing Rscript --version)\n* perl (check if installed by typing perl --version)\n* Mango Graph Studio for multi-network analysis\n\n## Installation\n\n```\ngit clone https://github.com/incertae-sedis/cavatica.git\n```\n\n## Basic Example\n\nHere is a basic example fetching PubMed and PMC papers containing the word \"Neo4j\" and \"Cytoscape\". \n\n```\ncd cavatica/data\nmkdir test\ncd test\necho \"Neo4j\" > config.txt\necho \"Cytoscape\" >> config.txt\n../../code/script.sh\n```\n\nThis will create tabular files (list of papers `Neo4j_papers_pm.tsv` and list of authors `Neo4j_authors_pm.tsv`). Open the png files `Neo4j_pm.png` to see a barchart of the number of papers by year.\n\n\n $\"Neo4j$ $\"Cavatica$ \n\nCan also open the html files to check the one sentence usages of Neo4j and Cavatica\n\n\n\n\n\n

Sentences that contain Neo4j

2018 29377902\n Reactome graph database: Efficient access to complex pathway data.

Here \nwe present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data.

2018 28936969 Systematic integration of biomedical knowledge prioritizes drugs for repurposing.

First, we constructed Hetionet (neo4j.het.io), an integrative network encoding knowledge from millions of biomedical studies.

2017 28416946 Use of Graph Database for the Integration of Heterogeneous Biological Data.

Here, we demonstrate the feasibility of using a graph-based database for complex biological relationships by comparing the performance between MySQL and Neo4j, one of the most widely used graph databases.
When we tested the query execution performance of MySQL versus Neo4j, we found that Neo4j outperformed MySQL in all cases.
These results show that using graph-based databases, such as Neo4j, is an efficient way to store complex biological relationships.

\n\n...\n

\n\n\n\n\n\n

Sentences that contain Cytoscape

2018 29894068 Identification of potential miRNAs and candidate genes of cervical intraepithelial neoplasia by bioinformatic analysis.

Then the miRNA- mRNA regulatory network was constructed using Cytoscape software.

2018 29872319 An integrated analysis of key microRNAs, regulatory pathways and clinical relevance in bladder cancer.

Protein-protein interaction (PPI) and miRNA-mRNA regulatory networks were established by using the Search Tool for the Retrieval of Interacting Genes/Proteins and Cytoscape tool.

2018 29760609 Identification of potential crucial genes and construction of microRNA-mRNA negative regulatory networks in osteosarcoma.

Protein-protein interaction (PPI) network was constructed by STRING and visualized in Cytoscape.

\n\n...\n

\n\nIt will also create a script `pubmed.gel`. Open [Mango Graph Studio](https://www.complexcomputation.com/en/product/mango-community-edition/), open `pubmed.gel` and type the following into the Mango Console.\n\n```\nrun \"pubmed.gel\";\n```\n\nThis will create a transition table and export the file. It will also load and visualize the author-paper networks.\n\n\n\n

Neo4j	Cytoscape\n
$\"Neo4j$	$\"Cavatica$ \n

\nGoing back to your terminal, rerun the script file and it will continue.\n\n```\n../../code/script.sh\n```\n\nThe transitions should be saved in `trends_pm.txt`. The following trends_pm.txt indicates that authors switched from cytoscape to Neo4j 9 times, while authors switched from Neo4j to Cytoscape 3 times.\n\n```\nCytoscape:Neo4j 9\nNeo4j:Cytoscape 3\n```\n\nIt will then commence searching PMC, fetching list of papers and authors and generating a \"pmc.gel\" file. Once again open the \"pmc.gel\" file in Mango and type the following into Mango Console.\n\n```\nrun \"pmc.gel\";\n```\n\nThen rerun the script to continue tabulating the trends which should be saved in `trends_pmc.txt`.\n\nThe output of a 2017 run comparing \"Neo4j\", \"Gephi\", \"GraphViz\" and \"iGraph\" is shown below:\n\n```\n=============PubMed Transitions\nNeo4j:Gephi 1\nNeo4j:GraphViz 1\nNeo4j:iGraph 1\n=============PubMed Central Transitions\nGephi:GraphViz 2\nGephi:Neo4j 3\nGephi:iGraph 31\nGraphViz:Gephi 19\nGraphViz:Neo4j 10\nGraphViz:iGraph 58\nNeo4j:Gephi 4\nNeo4j:GraphViz 4\nNeo4j:iGraph 1\niGraph:Gephi 34\niGraph:GraphViz 9\niGraph:Neo4j 13\n```\n\nPMC results usually return more papers since search terms like \"Neo4j\" or \"Cytoscape\" are being matched to the fulltext, instead of just the title and abstract. This may return more accurate trend tables since sometimes software names are only mentioned in the methods and not in the abstract.\n\n## Singularity Container\n\nThis repo provides a container for easily reproducing and running Cavatica through a container. The pipeline for both Singularity and Docker was ran on an Ubuntu 18.04 instance on [Jetstream](https://jetstream-cloud.org/), which is a national science and engineering cloud led by the Indiana University Pervasive Technology Institute.\n\nA singularity container of Cavatica is available on [Singularity Hub](https://singularity-hub.org/collections/1322). Using singularity you can download the contained with the following command:\n```\nsingularity pull shub://TeamMango/cavatica:latest\n```\nWhen run, the container will look for a text file called `config.txt` in a directory called `output` in the same directory as the `.simg` you just downloaded. Place the terms that you want Cavatica to search for in this file. In Ubuntu, you can use the following commands to create this file:\n```\nmkdir output\necho \"YOURSEARCHTERM\" > ./output/config.txt\n```\nYour search terms can also be followed by a year range, separated by commas:\n```\necho \"YOURSEARCHTERM,1996,2006\" > ./output/config.txt\n```\nEach search term and year range should occupy it's own line. If you want to search for use of the term cytoscape and VisANT between 1994 and 2000, `config.txt` would look like this:\n```\nvisant,1999,2006\ncytoscape,1994,2003\n```\nOnce you have entered the terms in the `config.txt` file, return to the same directory as the .simg image and run the following command:\n```\nsingularity run --bind output:/cavatica/data/output TeamMango-cavatica-master-latest.simg\n```\nThe results of the search will appear in the `output` directory next to your `config.txt` file.\n\n## Docker Container\nA docker container of Cavatica is available on [Docker Hub](https://hub.docker.com/r/incertaesedis/cavatica/). You can pull the docker container with the following command:\n\n```\ndocker pull incertaesedis/cavatica\n```\n\nTo run the docker container, move into the directory where you want to generate output from Cavatica. Create three files called `multitool-pubmed.tsv`, `multitool-pmc.tsv`, and `config.txt`. In Ubuntu you can do this with the following command:\n\n```\ntouch multitool-pubmed.tsv multitool-pmc.tsv config.txt\n```\n\nAll three files must be present in the directory where you run the container. In `config.txt` enter the search terms that you want Cavatica to search for, with each term on a new line. Optional year ranges can be indicated with commas:\n\n```\nvisant,1999,2006\ncytoscape,1994,2003\n```\n\nIn the same directory as config.txt, run the docker container:\n\n```\ndocker run -v ${PWD}:/cavatica/data/output incertaesedis/cavatica\n```\n\nIf on windows, `\"$PWD\"` should be replaced with the absolute path to your current directory. The files produced by Cavatica should appear on running the container. If you wish to rerun the search with different terms, make sure that the `multitool-pubmed.tsv` and `multitool-pmc.tsv` files are still in the folder. \n\n## Value of Reproducible Research\n[Accomplishments and opportunities of reproducing and containerizing this project](https://hackmd.io/s/r1Vxf9wVX)\n\n## Publications\n\n* J. Chang and H. Chou, \"[Cavatica: A pipeline for identifying author adoption trends among software or methods](https://www.computer.org/csdl/proceedings/bibm/2017/3050/00/08217990-abs.html),\" 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Kansas City, MO, USA, 2017, pp. 2145-2150.\n","has_starred","hub_user","immutable_tags_settings",{"_71":11,"_72":73},"enabled","rules",[74],".*","is_automated","permissions",{"_78":17,"_79":11,"_80":11},"read","write","admin","user","storage_size",4831560746,"orgData",{"_86":87,"_88":89,"_90":91,"_92":29,"_93":94,"_95":96,"_97":98,"_99":100,"_101":102,"_103":94,"_104":94,"_105":94,"_106":17},"id","c9d331fa600748d9bf6799ca5b06dc35","uuid","c9d331fa-6007-48d9-bf67-99ca5b06dc35","type","organization","orgname","full_name","","location","A good land","company","Incertae-sedis","profile_url","https://github.com/incertae-sedis","date_joined","2018-08-07T18:06:06.326818Z","gravatar_url","gravatar_email","badge","is_active","recentTags",[109],{"_110":40,"_111":112,"_113":114,"_86":115,"_116":117,"_46":134,"_135":112,"_136":29,"_137":52,"_53":138,"_139":140,"_141":125,"_142":134,"_143":61,"_144":17},"content_type","creator",3724695,"full_size",511621540,32611594,"images",[118],{"_119":120,"_121":122,"_123":94,"_124":125,"_126":127,"_128":129,"_130":94,"_131":-5,"_132":114,"_59":61,"_133":-5},"architecture","amd64","digest","sha256:17f0866a759026349e043060fe51a64fda3951929b70869e00029bcb145fbc15","features","last_pulled","2026-09-24T20:31:09.732166164Z","last_pushed","2019-09-23T00:48:25Z","os","linux","os_features","os_version","size","variant","2019-09-23T00:48:24.884609Z","last_updater","last_updater_username","media_type","latest","repository",5849614,"tag_last_pulled","tag_last_pushed","tag_status","v2","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","showSbxLogoOverride","sbxTrademarkText","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"routes/_layout.r.$namespace.$reponame.tags",{"_34":156,"_163":164,"_152":173,"_174":11},{"_36":157,"_38":158,"_41":42,"_43":44,"_45":11,"_46":47,"_48":49,"_50":159,"_53":31,"_28":29,"_54":55,"_56":40,"_57":58,"_59":58,"_60":61,"_62":-5,"_63":64,"_65":66,"_67":11,"_68":29,"_69":160,"_75":17,"_76":162,"_81":29,"_82":83},[],[40],[52],{"_71":11,"_72":161},[74],{"_78":17,"_79":11,"_80":11},"tags",{"_165":58,"_166":-5,"_167":-5,"_168":169},"count","next","previous","results",[170],{"_110":40,"_111":112,"_113":114,"_86":115,"_116":171,"_46":134,"_135":112,"_136":29,"_137":52,"_53":138,"_139":140,"_141":125,"_142":134,"_143":61,"_144":17},[172],{"_119":120,"_121":122,"_123":94,"_124":125,"_126":127,"_128":129,"_130":94,"_131":-5,"_132":114,"_59":61,"_133":-5},[],"canDeleteTags","actionData","errors"]

incertaesedis/cavatica

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