Crowd enabled curation and querying of large and noisy text mined protein interaction data

Jamil, Hasan M.; Sadri, Fereidoon

doi:10.1007/s10619-017-7209-x

Cited by 10 publications

(4 citation statements)

References 84 publications

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“…information extraction, named entity recognition) and document retrieval techniques, given the intractable publication volumes and intrinsic difficulties in professional curation, curators alone cannot ‘move the mountain’ that is ever growing ( 1 , 35 , 36 ). Alternative curation strategies have been proposed and used: crowd-sourcing ( 37 , 38 ) (see ( 39 ) on strategies of using crowd-sourced data that are of lower quality in general) and curation involving authors ( 35 , 36 ). In an experiment, the journal FEBS Letters requested consenting authors to submit a structured abstract, containing the identifiers of interacting proteins, their interaction types and the experimental method used.…”

Section: Related Workmentioning

confidence: 99%

Measurement Recorder: developing a useful tool for making species descriptions that produces computable phenotypes

et al. 2020

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To use published phenotype information in computational analyses, there have been efforts to convert descriptions of phenotype characters from human languages to ontologized statements. This postpublication curation process is not only slow and costly, it is also burdened with significant intercurator variation (including curator–author variation), due to different interpretations of a character by various individuals. This problem is inherent in any human-based intellectual activity. To address this problem, making scientific publications semantically clear (i.e. computable) by the authors at the time of publication is a critical step if we are to avoid postpublication curation. To help authors efficiently produce species phenotypes while producing computable data, we are experimenting with an author-driven ontology development approach and developing and evaluating a series of ontology-aware software modules that would create publishable species descriptions that are readily useable in scientific computations. The first software module prototype called Measurement Recorder has been developed to assist authors in defining continuous measurements and reported in this paper. Two usability studies of the software were conducted with 22 undergraduate students majoring in information science and 32 in biology. Results suggest that participants can use Measurement Recorder without training and they find it easy to use after limited practice. Participants also appreciate the semantic enhancement features. Measurement Recorder’s character reuse features facilitate character convergence among participants by 48% and have the potential to further reduce user errors in defining characters. A set of software design issues have also been identified and then corrected. Measurement Recorder enables authors to record measurements in a semantically clear manner and enriches phenotype ontology along the way. Future work includes representing the semantic data as Resource Description Framework (RDF) knowledge graphs and characterizing the division of work between authors as domain knowledge providers and ontology engineers as knowledge formalizers in this new author-driven ontology development approach.

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Section: Related Workmentioning

confidence: 99%

Measurement Recorder: developing a useful tool for making species descriptions that produces computable phenotypes

et al. 2020

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“…To be helpful for a certifiable application, a provenance framework ought to give offices to manipulate and query provenance data [2]. If a provenance framework handles transformations at different degrees of detail, it should provenance components for merging different transformations into one transformations and split an unpredictable change into an arrangement of less complex changes.…”

Section: A Query and Manipulation Functionalitiesmentioning

confidence: 99%

“…Where Cgas are the total transaction costs in gas, Nbytes is the contract size in bytes and Nwords is the number of 256 bit words that are initialized in the constructor. To calculate the deployment price in US-Dollar, the gas usage has to be multiplied with the the gasprice Pgas and the US-Dollar exchange rate for the ether Pexchange using equation (2).…”

Section: A Deployment Costsmentioning

confidence: 99%

Smart Contract: Data Provenance In Rice Supply Chain

Jyoti,

Chauhan

2020

IJRTE

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Before the invention of the various technologies, managing various activities and actions over the internet was achieved through a centralized server to guarantee valid data. With the expanding measure of accessible storage space and the quickening of data stream incited by the internet, a developing enthusiasm for data about the creation procedure and sources of information has developed. While this wide scope of use territories would profit by provenance data, the kind of provenance information, manipulation and querying facilities required vary from application to application. In this way, to discover the distinctions and similitudes between the different application and information model provenance needs and present a general plan for the arrangement of provenance. By characterizing this plan and applying it to existing work we plan to uncover open inquiries in the region of information provenance In this paper we survey the blockchain and provenance of the data in rice supplychain. We implement our proposed approach using smart contract which is to be deploy on ethereum blockchain network in rice supplychain to show the security and provenance of the data . We can track the progress of rice batch after each stage in blockchain and also discussed the need of provenance of assets in supplychain as it increase the trust of the customer

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“…e standard approach practiced in similar circumstances such as GitHub is to accept only administrator curated annotations, and allow local overriding by any user on their own without a ecting the community annotation. e second approach is to use an inaccurate model where the reliability of an annotation is dependent upon the combined credibility of all the curators who contributed to the annotation, an approach adopted in CrowdCure system [15]. e current edition of CodeMapper does not allow hypothetical concepts, or their implementation, to be included in a concept graph for a solution.…”

Section: Limitations and Future Improvementsmentioning

confidence: 99%

Computational thinking with the web crowd using Code Mapper

Vanvorce

Jamil

2019

Proceedings of the 34th ACM/SIGAPP Symposium on Applied Computing

Self Cite

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It has been argued that computational thinking should precede computer programming in the course of a career in computing. is argument is the basis for the slogan "logic rst, syntax later" and the development of many cryptic syntax removed programming languages such as Scratch!, Blockly and Visual Logic. e goal is to focus on the structuring of the semantic relationships among the logical building blocks to yield solutions to computational problems. While this approach is helping novice programmers and early learners, the gap between computational thinking and professional programming using high level languages such as C++, Python and Java is quite wide. It is wide enough for about one third students in rst college computer science classes to drop out or fail. In this paper, we introduce a new programming platform, called the CodeMapper, in which learners are able to build computational logic in independent modules and aggregate them to create complex modules. CodeMapper is an abstract development environment in which rapid visual prototyping of small to substantially large systems is possible by combining already developed independent modules in logical steps. e challenge we address involves supporting a visual development environment in which "annotated code snippets" authored by the masses in social computing sites such as SourceForge, StackOver ow or GitHub can also be used as is into prototypes and mapped to real executable programs. CodeMapper thus facilitates so transition from visual programming to syntax driven programming without having to practice syntax too heavily.

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Crowd enabled curation and querying of large and noisy text mined protein interaction data

Cited by 10 publications

References 84 publications

Measurement Recorder: developing a useful tool for making species descriptions that produces computable phenotypes

Measurement Recorder: developing a useful tool for making species descriptions that produces computable phenotypes

Smart Contract: Data Provenance In Rice Supply Chain

Computational thinking with the web crowd using Code Mapper

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