From fa2b89ad994d108a4f7bcaa4ff808e9715fa40f8 Mon Sep 17 00:00:00 2001 From: Tools Platform Ecosystem bot Date: Sun, 15 Oct 2023 01:08:41 +0000 Subject: [PATCH] import bio.tools data on Sun Oct 15 01:08:41 UTC 2023 --- data/drugsim2dr/drugsim2dr.biotools.json | 28 ++++++++ .../drugsim2dr_0.1.1.biotools.json | 26 ++++++++ data/mint/mint.biotools.json | 65 ++++++++++--------- data/qiime2/qiime2.biotools.json | 55 ++++++++++++++-- data/ular_toto/ular_toto.biotools.json | 13 ++++ 5 files changed, 151 insertions(+), 36 deletions(-) create mode 100644 data/drugsim2dr/drugsim2dr.biotools.json create mode 100644 data/drugsim2dr_0.1.1/drugsim2dr_0.1.1.biotools.json create mode 100644 data/ular_toto/ular_toto.biotools.json diff --git a/data/drugsim2dr/drugsim2dr.biotools.json b/data/drugsim2dr/drugsim2dr.biotools.json new file mode 100644 index 0000000000000..d51fbe4257006 --- /dev/null +++ b/data/drugsim2dr/drugsim2dr.biotools.json @@ -0,0 +1,28 @@ +{ + "additionDate": "2023-10-13T02:47:57.426429Z", + "biotoolsCURIE": "biotools:drugsim2dr", + "biotoolsID": "drugsim2dr", + "description": "A systematic biology tool was developed to repurpose drugs via a drug-drug functional similarity network. 'DrugSim2DR' first predict drug-drug functional similarity in the context of specific disease, and then using the similarity constructed a weighted drug similarity network. Finally, it used a network propagation algorithm on the network to identify drugs with significant target abnormalities as candidate drugs.", + "download": [ + { + "type": "Software package", + "url": "https://cran.r-project.org/web/src/contrib/DrugSim2DR_0.1.1.tar.gz", + "version": "0.1.1" + }, + { + "type": "Source code", + "url": "https://github.com/hanjunwei-lab/DrugSim2DR", + "version": "0.1.1" + } + ], + "editPermission": { + "type": "private" + }, + "homepage": "https://cran.r-project.org/web//packages/DrugSim2DR/index.html", + "lastUpdate": "2023-10-13T02:47:57.429884Z", + "name": "DrugSim2DR", + "owner": "Json", + "version": [ + "0.1.1" + ] +} diff --git a/data/drugsim2dr_0.1.1/drugsim2dr_0.1.1.biotools.json b/data/drugsim2dr_0.1.1/drugsim2dr_0.1.1.biotools.json new file mode 100644 index 0000000000000..7e4e707ccb695 --- /dev/null +++ b/data/drugsim2dr_0.1.1/drugsim2dr_0.1.1.biotools.json @@ -0,0 +1,26 @@ +{ + "additionDate": "2023-10-13T09:57:26.968130Z", + "biotoolsCURIE": "biotools:drugsim2dr_0.1.1", + "biotoolsID": "drugsim2dr_0.1.1", + "description": "A systematic biology tool was developed to repurpose drugs via a drug-drug functional similarity network. 'DrugSim2DR' first predict drug-drug functional similarity in the context of specific disease, and then using the similarity constructed a weighted drug similarity network. Finally, it used a network propagation algorithm on the network to identify drugs with significant target abnormalities as candidate drugs.", + "download": [ + { + "type": "Software package", + "url": "https://cran.r-project.org/web/packages/DrugSim2DR/" + }, + { + "type": "Source code", + "url": "https://github.com/hanjunwei-lab/DrugSim2DR" + } + ], + "editPermission": { + "type": "private" + }, + "homepage": "https://cran.r-project.org/web/packages/DrugSim2DR/", + "lastUpdate": "2023-10-13T09:57:26.970631Z", + "name": "DrugSim2DR_0.1.1", + "owner": "Json", + "version": [ + "0.1.1" + ] +} diff --git a/data/mint/mint.biotools.json b/data/mint/mint.biotools.json index 6d96b4c0399a8..2619645357c60 100644 --- a/data/mint/mint.biotools.json +++ b/data/mint/mint.biotools.json @@ -140,7 +140,7 @@ } ], "homepage": "https://mint.bio.uniroma2.it/", - "lastUpdate": "2020-12-16T10:07:53Z", + "lastUpdate": "2023-10-12T11:54:19.400490Z", "maturity": "Mature", "name": "MINT", "operatingSystem": [ @@ -192,7 +192,7 @@ "name": "Santonico E." } ], - "citationCount": 630, + "citationCount": 773, "date": "2012-01-01T00:00:00Z", "journal": "Nucleic Acids Research", "title": "MINT, the molecular interaction database: 2012 Update" @@ -204,33 +204,7 @@ ] }, { - "doi": "10.1002/cpbi.93", - "metadata": { - "abstract": "© 2020 John Wiley & Sons, Inc.The Molecular INTeractions Database (MINT) is a public database designed to store information about protein interactions. Protein interactions are extracted from scientific literature and annotated in the database by expert curators. Currently (October 2019), MINT contains information on more than 26,000 proteins and more than 131,600 interactions in over 30 model organisms. This article provides protocols for searching MINT over the Internet, using the new MINT Web Page. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Searching MINT over the internet. Alternate Protocol: MINT visualizer. Basic Protocol 2: Submitting interaction data.", - "authors": [ - { - "name": "Calderone A." - }, - { - "name": "Iannuccelli M." - }, - { - "name": "Licata L." - }, - { - "name": "Peluso D." - } - ], - "citationCount": 2, - "date": "2020-03-01T00:00:00Z", - "journal": "Current Protocols in Bioinformatics", - "title": "Using the MINT Database to Search Protein Interactions" - }, - "type": [ - "Method" - ] - }, - { + "doi": "10.1093/nar/gkt1115", "metadata": { "abstract": "IntAct (freely available at http://www.ebi.ac.uk/intact) is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. IntAct has developed a sophisticated web-based curation tool, capable of supporting both IMEx- and MIMIx-level curation. This tool is now utilized by multiple additional curation teams, all of whom annotate data directly into the IntAct database. Members of the IntAct team supply appropriate levels of training, perform quality control on entries and take responsibility for long-term data maintenance. Recently, the MINT and IntAct databases decided to merge their separate efforts to make optimal use of limited developer resources and maximize the curation output. All data manually curated by the MINT curators have been moved into the IntAct database at EMBL-EBI and are merged with the existing IntAct dataset. Both IntAct and MINT are active contributors to the IMEx consortium (http://www.imexconsortium.org). © 2013 The Author(s). Published by Oxford University Press.", "authors": [ @@ -340,7 +314,7 @@ "name": "Van Roey K." } ], - "citationCount": 886, + "citationCount": 1236, "date": "2014-01-01T00:00:00Z", "journal": "Nucleic Acids Research", "title": "The MIntAct project - IntAct as a common curation platform for 11 molecular interaction databases" @@ -349,6 +323,37 @@ "type": [ "Primary" ] + }, + { + "doi": "10.1002/cpbi.93", + "metadata": { + "abstract": "The Molecular INTeractions Database (MINT) is a public database designed to store information about protein interactions. Protein interactions are extracted from scientific literature and annotated in the database by expert curators. Currently (October 2019), MINT contains information on more than 26,000 proteins and more than 131,600 interactions in over 30 model organisms. This article provides protocols for searching MINT over the Internet, using the new MINT Web Page. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Searching MINT over the internet. Alternate Protocol: MINT visualizer. Basic Protocol 2: Submitting interaction data.", + "authors": [ + { + "name": "Calderone A." + }, + { + "name": "Iannuccelli M." + }, + { + "name": "Licata L." + }, + { + "name": "Peluso D." + } + ], + "citationCount": 13, + "date": "2020-03-01T00:00:00Z", + "journal": "Current Protocols in Bioinformatics", + "title": "Using the MINT Database to Search Protein Interactions" + }, + "type": [ + "Method" + ] + }, + { + "doi": "10.1093/nar/gkp983", + "pmid": "19897547" } ], "toolType": [ diff --git a/data/qiime2/qiime2.biotools.json b/data/qiime2/qiime2.biotools.json index 5b7e97bcb1822..a97c49a1686ea 100644 --- a/data/qiime2/qiime2.biotools.json +++ b/data/qiime2/qiime2.biotools.json @@ -1,12 +1,18 @@ { + "accessibility": "Open access", "additionDate": "2021-05-27T09:02:10Z", "biotoolsCURIE": "biotools:qiime2", "biotoolsID": "qiime2", + "confidence_flag": "tool", + "cost": "Free of charge", "credit": [ { "email": "greg.caporaso@nau.edu", "name": "Greg Caporaso", "orcidid": "https://orcid.org/0000-0002-8865-1670", + "typeRole": [ + "Primary contact" + ], "url": "https://caporasolab.us/" } ], @@ -34,7 +40,20 @@ "editPermission": { "type": "private" }, + "elixirCommunity": [ + "Galaxy" + ], "function": [ + { + "cmd": "deblur denoise-16S", + "note": "Deblur sequences using a 16S positive filter.\n\nPerform sequence quality control for Illumina data using the Deblur workflow with a 16S reference as a positive filter. Only forward reads are supported at this time. The specific reference used is the 88% OTUs from Greengenes 13_8. This mode of operation should only be used when data were generated from a 16S amplicon protocol on an Illumina platform. The reference is only used to assess whether each sequence is likely to be 16S by a local alignment using SortMeRNA with a permissive e-value; the reference is not used to characterize the sequences.", + "operation": [ + { + "term": "Sequencing quality control", + "uri": "http://edamontology.org/operation_3218" + } + ] + }, { "operation": [ { @@ -56,13 +75,20 @@ ] } ], - "homepage": "https://qiime2.org/", + "homepage": "https://qiime2.org", "language": [ "Python" ], - "lastUpdate": "2021-08-02T10:47:25Z", + "lastUpdate": "2023-10-12T19:54:24.104987Z", "license": "BSD-3-Clause", "link": [ + { + "note": "deblur denoise-16S Galaxy tool", + "type": [ + "Galaxy service" + ], + "url": "https://toolshed.g2.bx.psu.edu/repository/view_repository?id=167977019c8b8d17" + }, { "type": [ "Issue tracker" @@ -76,7 +102,8 @@ "url": "https://github.com/qiime2/qiime2" } ], - "name": "QIIME2.0", + "maturity": "Mature", + "name": "QIIME 2", "owner": "Kigaard", "publication": [ { @@ -420,18 +447,31 @@ "name": "von Hippel M." } ], - "citationCount": 1938, + "citationCount": 7952, "date": "2019-08-01T00:00:00Z", "journal": "Nature Biotechnology", "title": "Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2" }, "type": [ "Primary" - ] + ], + "version": "2.0" + } + ], + "relation": [ + { + "biotoolsID": "mafft", + "type": "uses" + }, + { + "biotoolsID": "qiime", + "type": "isNewVersionOf" } ], "toolType": [ - "Workbench" + "Command-line tool", + "Library", + "Suite" ], "topic": [ { @@ -450,5 +490,8 @@ "term": "Phylogeny", "uri": "http://edamontology.org/topic_0084" } + ], + "version": [ + "2.0" ] } diff --git a/data/ular_toto/ular_toto.biotools.json b/data/ular_toto/ular_toto.biotools.json new file mode 100644 index 0000000000000..d5ca8ac36a31c --- /dev/null +++ b/data/ular_toto/ular_toto.biotools.json @@ -0,0 +1,13 @@ +{ + "additionDate": "2023-10-12T12:12:52.620016Z", + "biotoolsCURIE": "biotools:ular_toto", + "biotoolsID": "ular_toto", + "description": "Ulartoto terpercaya merupakan situs yang sudah berlisensi resmi. Dengan min depo 5rb dan min bet 100 rupiah", + "editPermission": { + "type": "private" + }, + "homepage": "https://ularlucu.com/", + "lastUpdate": "2023-10-12T12:12:52.622834Z", + "name": "Ular toto", + "owner": "Ular.toto" +}