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import bio.tools data on Sun Oct 1 01:09:50 UTC 2023
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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|
@@ -12,6 +12,7 @@ | |
| "email": "[email protected]", | ||
| "name": "Christelle Dantec", | ||
| "orcidid": "https://orcid.org/0000-0001-7247-6460", | ||
| "rorid": "01xpc6869", | ||
| "typeEntity": "Person", | ||
| "typeRole": [ | ||
| "Primary contact" | ||
|
|
@@ -22,14 +23,15 @@ | |
| "email": "[email protected]", | ||
| "name": "Patrick Lemaire", | ||
| "orcidid": "https://orcid.org/0000-0003-4925-2009", | ||
| "rorid": "01xpc6869", | ||
| "typeEntity": "Person", | ||
| "typeRole": [ | ||
| "Primary contact" | ||
| ], | ||
| "url": "http://www.crbm.cnrs.fr/en/team/lemaire/" | ||
| }, | ||
| { | ||
| "email": "contact@aniseed.cnrs.fr", | ||
| "email": "[email protected]", | ||
| "typeRole": [ | ||
| "Support" | ||
| ] | ||
|
|
@@ -41,25 +43,25 @@ | |
| "type": [ | ||
| "API documentation" | ||
| ], | ||
| "url": "https://www.aniseed.cnrs.fr/api" | ||
| "url": "https://www.aniseed.fr/api" | ||
| }, | ||
| { | ||
| "type": [ | ||
| "Contributions policy" | ||
| ], | ||
| "url": "https://www.aniseed.cnrs.fr/aniseed/default/privacyPolicy" | ||
| "url": "https://www.aniseed.fr/aniseed/default/privacyPolicy" | ||
| }, | ||
| { | ||
| "type": [ | ||
| "Terms of use" | ||
| ], | ||
| "url": "https://www.aniseed.cnrs.fr/aniseed/default/termOfUse" | ||
| "url": "https://www.aniseed.fr/aniseed/default/termOfUse" | ||
| } | ||
| ], | ||
| "download": [ | ||
| { | ||
| "type": "Biological data", | ||
| "url": "https://www.aniseed.cnrs.fr/aniseed/download/download_data", | ||
| "url": "https://www.aniseed.fr/aniseed/download/download_data", | ||
| "version": "2019" | ||
| } | ||
| ], | ||
|
|
@@ -161,7 +163,7 @@ | |
| "PHP", | ||
| "Python" | ||
| ], | ||
| "lastUpdate": "2023-09-17T17:31:01.864728Z", | ||
| "lastUpdate": "2023-09-25T14:25:18.910230Z", | ||
| "license": "GPL-3.0", | ||
| "link": [ | ||
| { | ||
|
|
@@ -182,7 +184,13 @@ | |
| "type": [ | ||
| "Service" | ||
| ], | ||
| "url": "https://www.aniseed.cnrs.fr" | ||
| "url": "https://morphonet.org/" | ||
| }, | ||
| { | ||
| "type": [ | ||
| "Service" | ||
| ], | ||
| "url": "https://www.aniseed.fr" | ||
| } | ||
| ], | ||
| "maturity": "Mature", | ||
|
|
@@ -468,7 +476,7 @@ | |
| "name": "Yokomori R." | ||
| } | ||
| ], | ||
| "citationCount": 61, | ||
| "citationCount": 62, | ||
| "date": "2018-01-01T00:00:00Z", | ||
| "journal": "Nucleic Acids Research", | ||
| "title": "ANISEED 2017: Extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets" | ||
|
|
@@ -583,9 +591,94 @@ | |
| }, | ||
| { | ||
| "doi": "10.1093/nar/gkz955", | ||
| "type": [ | ||
| "Primary" | ||
| ], | ||
| "metadata": { | ||
| "abstract": "ANISEED (https://www.aniseed.cnrs.fr) is the main model organism database for the worldwide community of scientists working on tunicates, the vertebrate sister-group. Information provided for each species includes functionally-annotated gene and transcript models with orthology relationships within tunicates, and with echinoderms, cephalochordates and vertebrates. Beyond genes the system describes other genetic elements, including repeated elements and cis-regulatory modules. Gene expression profiles for several thousand genes are formalized in both wild-type and experimentally-manipulated conditions, using formal anatomical ontologies. These data can be explored through three complementary types of browsers, each offering a different view-point. A developmental browser summarizes the information in a gene- or territory-centric manner. Advanced genomic browsers integrate the genetic features surrounding genes or gene sets within a species. A Genomicus synteny browser explores the conservation of local gene order across deuterostome. This new release covers an extended taxonomic range of 14 species, including for the first time a non-ascidian species, the appendicularian Oikopleura dioica. Functional annotations, provided for each species, were enhanced through a combination of manual curation of gene models and the development of an improved orthology detection pipeline. Finally, gene expression profiles and anatomical territories can be explored in 4D online through the newly developed Morphonet morphogenetic browser.", | ||
| "authors": [ | ||
| { | ||
| "name": "Besnardeau L." | ||
| }, | ||
| { | ||
| "name": "Dantec C." | ||
| }, | ||
| { | ||
| "name": "Dardaillon J." | ||
| }, | ||
| { | ||
| "name": "Dauga D." | ||
| }, | ||
| { | ||
| "name": "Davidson B." | ||
| }, | ||
| { | ||
| "name": "Debiasse M.B." | ||
| }, | ||
| { | ||
| "name": "Douzery E." | ||
| }, | ||
| { | ||
| "name": "Dumollard R." | ||
| }, | ||
| { | ||
| "name": "Fagotto M." | ||
| }, | ||
| { | ||
| "name": "Faure E." | ||
| }, | ||
| { | ||
| "name": "Fujiwara S." | ||
| }, | ||
| { | ||
| "name": "Gueroult-Bellone M." | ||
| }, | ||
| { | ||
| "name": "Lemaire P." | ||
| }, | ||
| { | ||
| "name": "Louis A." | ||
| }, | ||
| { | ||
| "name": "Naville M." | ||
| }, | ||
| { | ||
| "name": "Nishida H." | ||
| }, | ||
| { | ||
| "name": "Nitta K.R." | ||
| }, | ||
| { | ||
| "name": "Onuma T.A." | ||
| }, | ||
| { | ||
| "name": "Reeves W." | ||
| }, | ||
| { | ||
| "name": "Roest Crollius H." | ||
| }, | ||
| { | ||
| "name": "Ryan J.F." | ||
| }, | ||
| { | ||
| "name": "Simion P." | ||
| }, | ||
| { | ||
| "name": "Veeman M." | ||
| }, | ||
| { | ||
| "name": "Volff J.-N." | ||
| }, | ||
| { | ||
| "name": "Wang K." | ||
| } | ||
| ], | ||
| "citationCount": 31, | ||
| "date": "2020-01-01T00:00:00Z", | ||
| "journal": "Nucleic Acids Research", | ||
| "title": "ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates" | ||
| }, | ||
| "version": "2019" | ||
| }, | ||
| { | ||
| "doi": "10.1093/nar/gkz955", | ||
| "version": "2019" | ||
| } | ||
| ], | ||
|
|
@@ -613,6 +706,14 @@ | |
| { | ||
| "biotoolsID": "interpro", | ||
| "type": "uses" | ||
| }, | ||
| { | ||
| "biotoolsID": "morphonet", | ||
| "type": "usedBy" | ||
| }, | ||
| { | ||
| "biotoolsID": "morphonet", | ||
| "type": "uses" | ||
| } | ||
| ], | ||
| "toolType": [ | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,108 @@ | ||
| { | ||
| "accessibility": "Open access", | ||
| "additionDate": "2023-09-25T12:40:15.653732Z", | ||
| "biotoolsCURIE": "biotools:celltrackvis", | ||
| "biotoolsID": "celltrackvis", | ||
| "confidence_flag": "tool", | ||
| "cost": "Free of charge", | ||
| "credit": [ | ||
| { | ||
| "email": "[email protected]", | ||
| "name": "Yon Dohn Chung", | ||
| "typeEntity": "Person" | ||
| } | ||
| ], | ||
| "description": "interactive browser-based visualization for analyzing cell trajectories and lineages.", | ||
| "documentation": [ | ||
| { | ||
| "type": [ | ||
| "Training material" | ||
| ], | ||
| "url": "http://scbeom.github.io/ctv_tutorial" | ||
| } | ||
| ], | ||
| "editPermission": { | ||
| "type": "private" | ||
| }, | ||
| "function": [ | ||
| { | ||
| "operation": [ | ||
| { | ||
| "term": "Cell migration analysis", | ||
| "uri": "http://edamontology.org/operation_3446" | ||
| }, | ||
| { | ||
| "term": "Simulation analysis", | ||
| "uri": "http://edamontology.org/operation_0244" | ||
| }, | ||
| { | ||
| "term": "Trajectory visualization", | ||
| "uri": "http://edamontology.org/operation_3890" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "homepage": "http://github.com/scbeom/celltrackvis", | ||
| "language": [ | ||
| "Python" | ||
| ], | ||
| "lastUpdate": "2023-09-25T12:40:15.656573Z", | ||
| "license": "GPL-3.0", | ||
| "name": "CellTrackVis", | ||
| "operatingSystem": [ | ||
| "Linux", | ||
| "Mac", | ||
| "Windows" | ||
| ], | ||
| "owner": "Pub2Tools", | ||
| "publication": [ | ||
| { | ||
| "doi": "10.1186/S12859-023-05218-Y", | ||
| "metadata": { | ||
| "abstract": "Background: Automatic cell tracking methods enable practitioners to analyze cell behaviors efficiently. Notwithstanding the continuous development of relevant software, user-friendly visualization tools have room for further improvements. Typical visualization mostly comes with main cell tracking tools as a simple plug-in, or relies on specific software/platforms. Although some tools are standalone, limited visual interactivity is provided, or otherwise cell tracking outputs are partially visualized. Results: This paper proposes a self-reliant visualization system, CellTrackVis, to support quick and easy analysis of cell behaviors. Interconnected views help users discover meaningful patterns of cell motions and divisions in common web browsers. Specifically, cell trajectory, lineage, and quantified information are respectively visualized in a coordinated interface. In particular, immediate interactions among modules enable the study of cell tracking outputs to be more effective, and also each component is highly customizable for various biological tasks. Conclusions: CellTrackVis is a standalone browser-based visualization tool. Source codes and data sets are freely available at http://github.com/scbeom/celltrackvis with the tutorial at http://scbeom.github.io/ctv_tutorial.", | ||
| "authors": [ | ||
| { | ||
| "name": "Choi Y.S." | ||
| }, | ||
| { | ||
| "name": "Chung Y.D." | ||
| }, | ||
| { | ||
| "name": "Kim D.Y." | ||
| }, | ||
| { | ||
| "name": "Kim W." | ||
| }, | ||
| { | ||
| "name": "Nguyen T.T.D." | ||
| }, | ||
| { | ||
| "name": "Shim C." | ||
| } | ||
| ], | ||
| "date": "2023-12-01T00:00:00Z", | ||
| "journal": "BMC Bioinformatics", | ||
| "title": "CellTrackVis: interactive browser-based visualization for analyzing cell trajectories and lineages" | ||
| }, | ||
| "pmcid": "PMC10053428", | ||
| "pmid": "36991341" | ||
| } | ||
| ], | ||
| "toolType": [ | ||
| "Desktop application" | ||
| ], | ||
| "topic": [ | ||
| { | ||
| "term": "Cell biology", | ||
| "uri": "http://edamontology.org/topic_2229" | ||
| }, | ||
| { | ||
| "term": "Imaging", | ||
| "uri": "http://edamontology.org/topic_3382" | ||
| }, | ||
| { | ||
| "term": "Literature and language", | ||
| "uri": "http://edamontology.org/topic_3068" | ||
| } | ||
| ] | ||
| } |
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