Contextual Data Management and Retrieval: A Self-organized Approach

2010 ◽  
pp. 145-162
Author(s):  
Gabriella Castelli ◽  
Franco Zambonelli
Keyword(s):  
Data Management ◽  
Contextual Data ◽  
Self Organized

scholarly journals Third-party Annotations: Linking PlutoF platform and the ELIXIR Contextual Data ClearingHouse for the reporting of source material annotation gaps and inaccuracies

2021 ◽  
Vol 5 ◽  
Author(s):  
Kessy Abarenkov ◽  
Allan Zirk ◽  
Kadri Põldmaa ◽  
Timo Piirmann ◽  
Raivo Pöhönen ◽  
...  
Keyword(s):  
Data Management ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Third Party ◽  
Web Interface ◽  
Material Source ◽  
Contextual Data ◽  
Management Platform ◽  
Wide Range

Third-party annotations are a valuable resource to improve the quality of public DNA sequences. For example, sequences in International Nucleotide Sequence Databases Collaboration (INSDC) often lack important features like taxon interactions, species level identification, information associated with habitat, locality, country, coordinates, etc. Therefore, initiatives to mine additional information from publications and link to the public DNA sequences have become common practice (e.g. Tedersoo et al. 2011, Nilsson et al. 2014, Groom et al. 2021). However, third-party annotations have their own specific challenges. For example, annotations can be inaccurate and therefore must be open for permanent data management. Further, every DNA sequence (except sequences from type material) can carry different species names, which must be databased as equal scientific hypotheses. PlutoF platform provides such data management services for third-party annotations. PlutoF is an online data management platform and computing service provider for biology and related disciplines. Registered users can enter and manage a wide range of data, e.g., taxon occurrences, metabarcoding data, taxon classifications, traits, and lab data. It also features an annotation module where third-party annotations (on material source, geolocation and habitat, taxonomic identifications, interacting taxa, etc.) can be added to any collection specimen, living culture or DNA sequence record. The UNITE Community is using these services to annotate and improve the quality of INSDC rDNA Internal Transcribed Spacer (ITS) sequence datasets. The National Center for Biotechnology Information (NCBI) is linking its ITS sequences with their annotations in PlutoF. However, there is still missing an automated solution for linking annotations in PlutoF with any sequence and sample record stored in INSDC databases. One of the ambitions of the BiCIKL Project is to solve this through operating the ELIXIR Contextual Data ClearingHouse (CDCH). CDCH offers a light and simple RESTful Application Programming Interface (API) to enable extension, correction and improvement of publicly available annotations on sample and sequence records available in ELIXIR data resources. It facilitates feeding improved or corrected annotations from databases (such as secondary databases, e.g., PlutoF, which consume and curate data from repositories) back to primary repositories (databases of the three INSDC collaborative partners). In the Biodiversity Community Integrated Knowledge Library (BiCIKL) Project, the University of Tartu Natural History Museum is leading the task of linking the two components—the web interface provided by the PlutoF platform and CDCH APIs—to allow user-friendly and effortless reporting of errors and gaps in sequenced material source annotations. The API and web interface will be promoted to those communities (such as taxonomists, those abstracting from the literature, and those already using the community curated data) with the appropriate knowledge and tools who will be encouraged to report their enhanced annotations back to primary repositories.

Problem behavior in autism spectrum disorders: A paradigmatic self-organized perspective of network structures

2019 ◽  
Vol 42 ◽  
Author(s):  
Lucio Tonello ◽  
Luca Giacobbi ◽  
Alberto Pettenon ◽  
Alessandro Scuotto ◽  
Massimo Cocchi ◽  
...  
Keyword(s):  
Autism Spectrum Disorder ◽  
Problem Behaviors ◽  
Autism Spectrum ◽  
The Self ◽  
Network Structures ◽  
Self Organized ◽  
Critical Equilibrium ◽  
Self Organized Criticality ◽  
Acute Agitation ◽  
Spectrum Disorders

AbstractAutism spectrum disorder (ASD) subjects can present temporary behaviors of acute agitation and aggressiveness, named problem behaviors. They have been shown to be consistent with the self-organized criticality (SOC), a model wherein occasionally occurring “catastrophic events” are necessary in order to maintain a self-organized “critical equilibrium.” The SOC can represent the psychopathology network structures and additionally suggests that they can be considered as self-organized systems.

Dynamics of Self-Organized and Self-Assembled Structures

2009 ◽  
Author(s):  
Rashmi C. Desai ◽  
Raymond Kapral
Keyword(s):  
Self Organized ◽  
Self Assembled
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