scholarly journals Pure for me or impure for us: Pollution in the Gene Regulation Knowledge Commons

2020 ◽  
Author(s):  
Anamika Chatterjee
Keyword(s):  
Gene Regulation ◽  
Knowledge Management ◽  
Natural Resources ◽  
Data Management ◽  
Life Science ◽  
Science Knowledge ◽  
Knowledge Commons ◽  
Standard Framework

Pollution has been a common threat to the sustainability of commons resources. While there now exist plenty of safeguards addressing the consequences of pollution on natural resources, little attention has been given to those on the knowledge commons. To understand how pollution occurs and is tackled in the knowledge commons, I take the case of a subset of the life science knowledge commons – the Gene Regulation Knowledge Commons (GRKC). Members from the gene regulation community have come together to work towards a knowledge commons under the Gene Regulation Ensemble Effort for the Knowledge Commons (“GREEKC”). Their efforts have been directed at coordinating and aligning the various practices of data management that prevail across different databases pertaining to gene regulation knowledge. The end goal is to establish a standard framework for knowledge management for GRKC. By examining the polluting practices that arise in the GRKC and how this pollution is alleviated, I claim that here, manually curated databases discern between knowledge that is pure or polluted. However, being a part of the same commons do these databases draw the same distinctions between what is pure and what is polluted? Or do different databases arrive at different conclusions? Is what is pure for one also pure for all?

Emergent Ontologies by Collaborative Tagging for Knowledge Management

2013 ◽  
pp. 54-69 ◽  
Author(s):  
Weena Jimenez ◽  
César Luis Alvargonzález ◽  
Pablo Abella Vallina ◽  
Jose María Álvarez Gutiérrez ◽  
Patricia Ordóñez de Pablos ◽  
...  
Keyword(s):  
Social Networks ◽  
Knowledge Management ◽  
Data Management ◽  
Dynamic Environment ◽  
Information Resources ◽  
The Other ◽  
Specific Domain ◽  
Ontology Modeling ◽  
Web Information ◽  
Use Of Internet

The massive use of Internet and social networks leads us to a new dynamic environment with huge amounts of unstructured and unclassified information resources in continuous evolution. New classification, compilation, and recommendation systems based on the use of folksonomies and ontologies have appeared to deal with the requirements of data management in this environment. Nevertheless, using ontologies alone has some weaknesses due to the need of being statically modeled by a set of experts in a specific domain. On the other hand, folksonomies show a lack of formality because of their implicit ambiguity and flexibility by definition. The main objective of this chapter is to outline and evaluate a new way to exploit Web information resources and tags for bridging the gap between ontology modeling and folksonomies.

Towards The New Episteme

2013 ◽  
pp. 45-59
Author(s):  
Zbigniew Król
Keyword(s):  
Knowledge Management ◽  
Tacit Knowledge ◽  
Philosophy Of Language ◽  
Explicit Knowledge ◽  
Professional Collaboration ◽  
Science Knowledge ◽  
Types Of Knowledge ◽  
New Knowledge ◽  
Definition Of ◽  
The Given

The usual horizon of knowledge science is limited to nominalism, empiricism, and naturalistic and evolutionary epistemologies. I propose to broaden this horizon by applying some other philosophical attitudes, such as a non-nominalistic philosophy of language. A basic methodology for the new episteme, including (non-nominalistic) typology and a definition of knowledge and of tacit knowledge, is proposed. Several types of knowledge and the corresponding tacit knowledge are discussed within a broadened philosophical context. There are many types of knowledge and tacit knowledge using different methods of sharing. The main problem with the effective sharing of tacit knowledge is sharing knowledge relevant to the given problem. The transfer, change and transformation of tacit knowledge into explicit knowledge are possible. An example of such a transition, which I call conceptualization, is described. Conceptualization exemplifies how new knowledge can be created with the use of tacit knowledge. A need also exists for a professional collaboration between knowledge science, knowledge management and philosophy.

Towards The New Episteme

2010 ◽  
Vol 1 (1) ◽  
pp. 43-57
Author(s):  
Zbigniew Król
Keyword(s):  
Knowledge Management ◽  
Tacit Knowledge ◽  
Philosophy Of Language ◽  
Explicit Knowledge ◽  
Professional Collaboration ◽  
Science Knowledge ◽  
Types Of Knowledge ◽  
New Knowledge ◽  
Definition Of ◽  
The Given

The usual horizon of knowledge science is limited to nominalism, empiricism, and naturalistic and evolutionary epistemologies. I propose to broaden this horizon by applying some other philosophical attitudes, such as a non-nominalistic philosophy of language. A basic methodology for the new episteme, including (nonnominalistic) typology and a definition of knowledge and of tacit knowledge, is proposed. Several types of knowledge and the corresponding tacit knowledge are discussed within a broadened philosophical context. There are many types of knowledge and tacit knowledge using different methods of sharing. The main problem with the effective sharing of tacit knowledge is sharing knowledge relevant to the given problem. The transfer, change and transformation of tacit knowledge into explicit knowledge are possible. An example of such a transition, which I call conceptualization, is described. Conceptualization exemplifies how new knowledge can be created with the use of tacit knowledge. A need also exists for a professional collaboration between knowledge science, knowledge management and philosophy.

Inter-laboratory calibration of a Ag3PO4 comparison material for oxygen stable isotope analysis

2020 ◽  
Author(s):  
Andrea Watzinger ◽  
Katharina Schott ◽  
Rebecca Hood-Nowotny ◽  
Grzegorz Skrzypek ◽  
Federica Tamburini ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Temperature ◽  
Stable Isotope ◽  
Natural Resources ◽  
Life Science ◽  
Arithmetic Mean ◽  
Environmental Research ◽  
Weighted Arithmetic ◽  
Laboratory Calibration ◽  
The University

<p>A silver phosphate comparison material (Ag<sub>3</sub>PO<sub>4</sub>) for measurement of the stable oxygen isotope composition was prepared by the University of Natural Resources and Life Science (BOKU) and distributed to four international isotope laboratories frequently measuring the δ<sup>18</sup>O value in Ag<sub>3</sub>PO<sub>4</sub>. The contributing laboratories were the University of Natural Resources and Life Science (BOKU), The University of Western Australia (UWA), the ETH Zurich (ETH), the University of Helsinki (UH) and the Helmholtz Centre for Environmental Research (UFZ). Each laboratory analysed the comparison material in a minimum of two independent measuring rounds with a minimum of 10 individual measurements. The instrument used to perform the measurements were high-temperature conversion elemental analyzers coupled with continuous flow isotope ratio mass spectrometers: TC/EA with Thermo Finnigan Delta XP (BOKU), a TC/EA with a Thermo Scientific Delta V Plus (UWA), an Elementar Pyrocube with a Isoprime 100 (ETH), a Flash IRMS EA with a Thermo Scientific Delta V Plus (UH) and a TC/EA with a Finnigan Delta S (UFZ). The working gas δ<sup>18</sup>O was set to 0 ‰ and the normalization was done by a three-point linear regression calibration (Paul et al., 2007) using the reference material IAEA-601 (δ<sup>18</sup>O<sub>VSMOW</sub> = +23.14 ± 0.17 ‰), IAEA-602 (δ<sup>18</sup>O<sub>VSMOW</sub> = +71.28 ±0.42 ‰) (both benzoic acid) and NBS 127 (barium sulfate) (δ<sup>18</sup>O<sub>VSMOW</sub> = +8.59 ± 0.20 ‰) (Brand et al., 2009). BOKU, UH and ETH had experienced inhomogeneity of the IAEA-602 as already mentioned in Brand et al. (2009). The weighted arithmetic mean and standard deviation (1σ) of the new BOKU Ag<sub>3</sub>PO<sub>4</sub> comparison material from the single measurements has a δ<sup>18</sup>O value of 13.80 ± 0.40 ‰ on the VSMOW scale (n=131), while the median of the single rounds was 13.76 ‰ (n=11) and the median of the laboratories was 13.79 ‰ (n=5). The arithmetic means of two measuring rounds were outside ± 1σ. When excluding data from these rounds from the statistics the weighted arithmetic mean has a δ<sup>18</sup>O value of 13.80 ± 0.32 ‰ on the VSMOW scale (n = 111) and the median of the single valid rounds (n=9) remained at 13.76 ‰ and the median of the labs at 13.79 ‰ (n=5). Excluding NBS127 from the normalization slightly reduced the δ<sup>18</sup>O value to 13.74 ± 0.31 ‰ (n = 111). The BOKU Ag<sub>3</sub>PO<sub>4</sub> comparison material is available for stable isotope research laboratories to facilitate the calibration of their lab comparison material.</p><p> </p><p>Brand, W.A., Coplen, T.B., Aerts-Bijma, A.T., Böhlke, J.K., Gehre, M., Geilmann, H., Gröning, M., Jansen, H.G., Meijer, H.A.J., Mroczkowski, S.J., Qi, H., Soergel, K., Stuart-Williams, H., Weise, S.M., Werner, R.A., 2009. Comprehensive inter-laboratory calibration of reference materials for δ<sup>18</sup>O versus VSMOW using various on-line high-temperature conversion techniques. Rapid Communications in Mass Spectrometry, 999–1009. doi:10.1002/rcm</p><p>Paul, D., Skrzypek, G., Fórizs, I., 2007. Normalization of measured stable isotopic compositions to isotope reference scales - A review. Rapid Communications in Mass Spectrometry 21, 3006–3014. doi:10.1002/rcm.3185</p>

scholarly journals Gene regulation knowledge commons: community action takes care of DNA binding transcription factors

Database ◽  
2016 ◽  
Vol 2016 ◽  
pp. baw088 ◽  
Author(s):  
Sushil Tripathi ◽  
Steven Vercruysse ◽  
Konika Chawla ◽  
Karen R. Christie ◽  
Judith A. Blake ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Transcription Factors ◽  
Dna Binding ◽  
Community Action ◽  
Knowledge Commons

scholarly journals pISA-tree - a data management framework for life science research projects using a standardised directory tree

2021 ◽  
Author(s):  
Marko Petek ◽  
Maja Zagorscak ◽  
Andrej Blejec ◽  
Ziva Ramsak ◽  
Anna Coll ◽  
...  
Keyword(s):  
Data Management ◽  
Life Science ◽  
Source Code ◽  
Science Research ◽  
Open Science ◽  
Reproducible Research ◽  
Public Repository ◽  
Management Framework ◽  
Fair Principles ◽  
R Packages

We have developed pISA-tree, a straightforward and flexible data management solution for organisation of life science project-associated research data and metadata. It enables on-the-fly creation of enriched directory tree structure (project/Investigation/Study/Assay) via a series of sequential batch files in a standardised manner based on the ISA metadata framework. The system supports reproducible research and is in accordance with the Open Science initiative and FAIR principles. Compared with similar frameworks, it does not require any systems administration and maintenance as it can be run on a personal computer or network drive. It is complemented with two R packages, pisar and seekr, where the former facilitates integration of the pISA-tree datasets into bioinformatic pipelines and the latter enables synchronisation with the FAIRDOMHub public repository using the SEEK API. Source code and detailed documentation of pISA-tree and its supporting R packages are available from https://github.com/NIB-SI/pISA-tree.

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