Main Page: Difference between revisions

From BugSigDB
(get rid of "Beta version")
(Improve writing of top paragraph.)
 
(9 intermediate revisions by 2 users not shown)
Line 5: Line 5:
</div>
</div>


BugSigDB.org is a community-editable [https://www.semantic-mediawiki.org Semantic Mediawiki knowledge management system] that simplifies and standardizes the recording, finding, and re-analysis of differential abundance results from all types of metagenomics studies. To contribute please [[Special:RequestAccount|request an account]], [[Help:Contents|learn how to contribute or analyze]], [[Project:About|learn more about the project]], [https://github.com/waldronlab/BugSigDB/discussions provide feedback], or [https://github.com/waldronlab/BugSigDB/issues report issues].
BugSigDB.org (published in '''[https://www.nature.com/articles/s41587-023-01872-y Nature Biotechnology''']) is a community-editable [https://www.semantic-mediawiki.org Semantic Mediawiki knowledge management system]. Its primary functions include '''1. standardization''' of key elements of published microbiome studies using ontologies and the NCBI taxonomy, '''2. [https://bugsigdb.org/Special:RunQuery/Drill?Drill%5BCondition%20logic%5D=AND&Drill%5BLocation%20logic%5D=AND&Drill%5BSite%20logic%5D=AND&_run=1 searchability]''', '''3. Enrichment Analysis''' using [[Help:Export|bulk exports]], [https://github.com/waldronlab/BugSigDBExports GMT files], or other software (e.g. [https://bioconductor.org/packages/bugsigdbr/ bugsigdbr]), and '''4. community interaction:''' you can [[Special:RequestAccount|request an account]], [[Help:Contents|contribute or analyze]], learn [[Project:About|about]] the project, [https://github.com/waldronlab/BugSigDB/issues report issues], and ask questions on the [https://community-bioc.slack.com/archives/C04RATV9VCY/p1697144958544289 #bugsigdb channel] of the [https://slack.bioconductor.org/ community-bioc Slack team]. This collaborative effort aims to accelerate microbiome research by providing a comprehensive database of microbial signatures from published studies, along with relevant information on study design and geography, health outcomes, host body site, and experimental methods.


[[Project:About|<span class="mw-ui-button mw-ui-progressive float-right mt-3">About this project</span>]]
[[Project:About|<span class="mw-ui-button mw-ui-progressive float-right mt-3">About this project</span>]]
Line 36: Line 36:
<div class="card-header text-secondary px-3 py-2 font-weight-bold">Statistics</div>
<div class="card-header text-secondary px-3 py-2 font-weight-bold">Statistics</div>
<div class="card-body">
<div class="card-body">
* <b>{{#ask: [[Category:Studies]][[Modification date::+]]|format=count }}</b> studies
{{MediaWiki:Statistics-footer}}
* <b>{{#ask: [[Category:Signatures]][[Modification date::+]]|format=count }}</b> signatures
* <b>{{#show: Project:Unique taxa index |?Unique taxa index# }}</b> unique taxa
* <b>{{#expr: {{#arraymap: {{#show: Property:Host species |?Allows value }}
    |,
    |@
    |{{#if: {{#ask: [[Category:Experiments]][[Modification date::+]][[Host species::@]]|limit=1|searchlabel=-}}
      |1
      |0
    }}
    |+
  }}}}</b> host species
* {{#arraydefine: locations
    |{{#ask: [[Category:Experiments]][[Modification date::+]][[Location of subjects::+]]
      |?Location of subjects
      |mainlabel=-
      |headers=hide
      |sep=;
      |manysep=;
      |format=array
      |limit=10000
      |searchlabel=
    }}
    |;
    |unique
  }}<b>{{#arraysize: locations|;}}</b>  locations
* {{#arraydefine: bodysites
    |{{#ask: [[Category:Experiments]][[Modification date::+]][[Body site::+]]
      |?Body site
      |mainlabel=-
      |headers=hide
      |sep=;
      |manysep=;
      |format=array
      |limit=10000
      |searchlabel=
    }}
    |;
    |unique
  }}<b>{{#arraysize: bodysites|;}}</b> body sites
* {{#arraydefine: conditions
    |{{#ask: [[Category:Experiments]][[Modification date::+]][[Condition::+]]
      |?Condition
      |mainlabel=-
      |headers=hide
      |sep=;
      |manysep=;
      |format=array
      |limit=10000
    }}
    |;
    |unique
  }}<b>{{#arraysize: conditions|;}}</b> study conditions
* contributed by {{#arraydefine: curators
    |{{#ask: [[Category:Experiments]][[Modification date::+]][[Curator::+]]
      |?Curator
      |mainlabel=-
      |headers=hide
      |sep=;
      |manysep=;
      |format=array
      |limit=10000
      |searchlabel=
    }}
    |;
    |unique
  }}<b>{{#arraysize: curators|;}}</b> curators
</div>
</div>
<div class="card-footer py-2">{{#queryformlink: form=Drilldown|link text=<span class="mw-ui-button mw-ui-quiet text-primary pl-0 pr-1">Browse all studies</span>|_run=1}} <small>by Host species {{!}} Body site {{!}} Condition {{!}} Taxa {{!}} Location of subjects.</small>
<div class="card-footer py-2">{{#queryformlink: form=Drilldown|link text=<span class="mw-ui-button mw-ui-quiet text-primary pl-0 pr-1">Browse all studies</span>|_run=1}} <small>by Host species {{!}} Body site {{!}} Condition {{!}} Taxa {{!}} Location of subjects.</small>

Latest revision as of 14:32, 21 February 2024

BugSigDB

A Comprehensive Database of Published Microbial Signatures

BugSigDB.org (published in Nature Biotechnology) is a community-editable Semantic Mediawiki knowledge management system. Its primary functions include 1. standardization of key elements of published microbiome studies using ontologies and the NCBI taxonomy, 2. searchability, 3. Enrichment Analysis using bulk exports, GMT files, or other software (e.g. bugsigdbr), and 4. community interaction: you can request an account, contribute or analyze, learn about the project, report issues, and ask questions on the #bugsigdb channel of the community-bioc Slack team. This collaborative effort aims to accelerate microbiome research by providing a comprehensive database of microbial signatures from published studies, along with relevant information on study design and geography, health outcomes, host body site, and experimental methods.

About this project

NCBI.png 1573535Featured Taxon
Holdemanella(genus)
cellular organismsBacteriaBacillatiBacillotaErysipelotrichiaErysipelotrichalesErysipelotrichaceae
BugSigDB Statistics
  • Number of studies: 38 (filter)
  • Number of signatures: 53
  • Number of direct descendants: 3
Study by nameFeatured Studies
Association of dietary fibre intake and gut microbiota in adults
The British journal of nutrition, 2018 | Feces | Diet | United States of America
Gut Microbiome Influences the Efficacy of PD-1 Antibody Immunotherapy on MSS-Type Colorectal Cancer via Metabolic Pathway
Frontiers in microbiology, 2020 | Feces | Antimicrobial agent | China

Taxa

Fuzzy | Parameterized | Logical operators » ExampleAdvanced Search
Statistics
  • 1399 studies
  • 7582 signatures
  • 2195 unique taxa
  • 44 host species
  • 94 locations
  • 173 body sites
  • 518 conditions
  • contributed by 178 contributors
Browse all studies by Host species | Body site | Condition | Taxa | Location of subjects.
Top 5 Contributors in the last 30 days

Last 30 days (Top 5)
RankScorePagesChangesUsername
1 659 656 658 Svetlana up
2 392 343 938 Tosin
3 174 153 264 MyleeeA
4 120 75 588 Joiejoie
5 88 78 105 KateRasheed
Extended Statistics
Retrieved from "https://bugsigdb.org/w/index.php?title=Main_Page&oldid=120834"
The City University of New York
Bioconductor - Open Source Software for Bioinformatics
WikiWorks
Powered by MediaWiki
Powered by Semantic MediaWiki