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Reactome Pengine: a web-logic API to the Homo sapiens reactome

Samuel R Neaves, Sophia Tsoka, Louise A C Millard, Oliver Stegle
2018 Bioinformatics  
Reactome Pengine is a web service providing a logic programming-based API to the human reactome.  ...  Either a researcher is restricted to particular queries defined by a web application programming interface (API) or they have to download the whole database.  ...  Pengines allows data providers to make their Prolog knowledge base available to users via a web service [that uses a web-logic API (Lager and Wielemaker, 2014) ], accessed as if it was on the user's machine  ... 
doi:10.1093/bioinformatics/bty181 pmid:29617950 pmcid:PMC6084589 fatcat:suo5ixv3yfbgfpygzcycd57ene

Pertuniti: Subprocess modeling and hierarchic case management

Johannes Tenschert, Sophia Marmaridis
2020 International Conference on Business Process Management  
Today, adaptive case management is typically either tailored towards flexible process models or ad-hoc activities for a lot size of 1.  ...  Pertuniti connects both approaches by implementing cases as a set primarily of groupware artifacts for complete flexibility, subprocess modeling to automate aspects of the work, and flexible case data  ...  Technical details Pertuniti is a single-page web application written in Angular and Typescript on the client side, and primarily Java on the server side.  ... 
dblp:conf/bpm/TenschertM20 fatcat:jeku5si5wjhndmgeegsq2is6ba

AmalgamScope: Merging Annotations Data across the Human Genome

Georgia Tsiliki, Konstantinos Tsaramirsis, Sophia Kossida
2014 BioMed Research International  
Additionally, users can define custom transcriptome library files for any species and use the file exchanging distant server options of the tool.  ...  Their sheer volume and different data scope pose a challenge to jointly visualize and integrate diverse data types.  ...  Our software provides a flexible framework to summarize fragmented annotation information across data types, relative to information extracted from web-based annotation resources, providing a common platform  ... 
doi:10.1155/2014/893501 pmid:24967409 pmcid:PMC4055292 fatcat:b6f7uj442nhfrd6edjhp6ypfda

Speeding up Web Page Loads with Shandian

Xiao Sophia Wang, Arvind Krishnamurthy, David Wetherall
2016 Symposium on Networked Systems Design and Implementation  
These solutions require knowledge of dependencies between Web objects within a page beforehand to build a prioritization plan.  ...  Shandian prioritizes Web contents at a finer granularity and does not require the system to obtain any knowledge of the Web pages beforehand.  ... 
dblp:conf/nsdi/WangKW16 fatcat:6vowwzcmivae7noaaxr62exoz4


Sophia Yang, Marc Skov Madsen, James A. Bednar
2022 Proceedings of the 28th ACM SIGKDD Conference on Knowledge Discovery and Data Mining  
tools for your data and models without having to run a web-technology software development project, and finally how to deploy your dashboard.  ...  You will learn how to turn nearly any notebook into a deployable dashboard, how to build visualizations easily even for big, streaming, and multidimensional data, how to build interactive drill-down exploratory  ...  It provides the flexibility to choose among several API backends, including bokeh, matplotlib, and plotly, so you can choose different backends based on your preferences.  ... 
doi:10.1145/3534678.3542621 fatcat:7rqnm6ar6be23m7m67a2cvru7u

Development and Analysis of NLP Pipelines in Argo

Rafal Rak, Andrew Rowley, Jacob Carter, Sophia Ananiadou
2013 Annual Meeting of the Association for Computational Linguistics  
In this paper, we demonstrate Argo, a Web-based workbench for the development and processing of NLP pipelines/workflows.  ...  The workbench is based upon UIMA, and thus has the potential of using many of the existing UIMA resources.  ...  Such a knowledge base can be queried with languages such as SPARQL 8 , an official W3C Recommendation.  ... 
dblp:conf/acl/RakRCA13 fatcat:xd5bycssxfaldihitemy3urody

Measuring and predicting web login safety

Xiao Sophia Wang, David Choffnes, Patrick Gage Kelley, Ben Greenstein, David Wetherall
2011 Proceedings of the first ACM SIGCOMM workshop on Measurements up the stack - W-MUST '11  
Based on a measurement study using login pages gathered from popular sites in addition to those visited by users through normal Web browsing, we found such predictions to be quite challenging due to a  ...  lack of any standard formats for Web logins.  ...  to a server.  ... 
doi:10.1145/2018602.2018616 dblp:conf/sigcomm/WangCKGW11 fatcat:m6bmmwfxdbhajk3kdmfg57arwi

Challenges and Directions in Knowledge Asset Trading [chapter]

Dimitris Apostolou, Gregory Mentzas, Andreas Abecker, Wolf-Christian Eickhoff, Wolfgang Maas, Panos Georgolios, Kostas Kafentzis, Sophia Kyriakopoulou
2002 Lecture Notes in Computer Science  
The paper describes the business challenges associated with the design of Internet-based knowledge marketplace.  ...  INKASS, a European IST project, has stimulated this work and has provided real-life verification on the arguments raised and on the positions adopted herein.  ...  Standards HTTP servers and XML enhanced Web content are proving effective (, 2002) as the foundation for small groups of co-operating commerce agents operating over the Internet.  ... 
doi:10.1007/3-540-36277-0_48 fatcat:nwqmyyupgreczj6aqwxc2c5dkm

Multi-PoP Network Slice Deployment: A Feasibility Study

Polychronis Valsamas, Panagiotis Papadimitriou, Ilias Sakellariou, Sophia Petridou, Lefteris Mamatas, Stuart Clayman, Francesco Tusa, Alex Galis
2019 2019 IEEE 8th International Conference on Cloud Networking (CloudNet)  
In this paper, we present the design and prototype implementation of a network slicing architecture, based on which we perform a feasibility study of network slicing using multiple experimental infrastructures  ...  Network slicing is seen as a key enabler for meeting the diverse network service requirements, which stem from the transition to 5G.  ...  CPU, RAM utilization and storage usage) for each Web server.  ... 
doi:10.1109/cloudnet47604.2019.9064124 dblp:conf/cloudnet/Valsamas0SPMCTG19 fatcat:qqf7vobgubcmlnn46z5pmxyrpq

APLenty: annotation tool for creating high-quality datasets using active and proactive learning

Minh-Quoc Nghiem, Sophia Ananiadou
2018 Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing: System Demonstrations  
APLenty is highly flexible and can be adapted to various other tasks.  ...  A major innovation of our tool is the integration of automatic annotation with active learning and proactive learning.  ...  WebAnno offers a purely web-based generic annotation tool and supports distributed annotation.  ... 
doi:10.18653/v1/d18-2019 dblp:conf/emnlp/NghiemA18 fatcat:6zixjynefrd5rbbpl267p5mmie

rBEFdata: documenting data exchange and analysis for a collaborative data management platform

Claas-Thido Pfaff, Birgitta König-Ries, Anne C. Lang, Sophia Ratcliffe, Christian Wirth, Xingxing Man, Karin Nadrowski
2015 Ecology and Evolution  
We are witnessing a growing gap separating primary research data from derived data products presented as knowledge in publications.  ...  A batched download is available as well which works along a paper proposal mechanism implemented by BEFdata.  ...  Other options are dedicated to the URL of a TemaTres vocabulary server and the name of a download folder.  ... 
doi:10.1002/ece3.1547 pmid:26306174 pmcid:PMC4541993 fatcat:qmxwerny6negdeolb4e5nersoi

Local Collaborations

Verna B. McKenna, Julia E. Gunn, John Auerbach, Kathryn H. Brinsfield, K. Sophia Dyer, M. Anita Barry
2003 Journal of Public Health Management and Practice  
Interpretation is based on the site contact’s knowledge of site norms.  ...  The form collects qualitative information based on the knowledge of the site contact.  ... 
doi:10.1097/00124784-200309000-00009 pmid:15503603 fatcat:7hicm2fxqvbj3bechlptx4ppfu

Structuring and extracting knowledge for the support of hypothesis generation in molecular biology

Marco Roos, M Scott Marshall, Andrew P Gibson, Martijn Schuemie, Edgar Meij, Sophia Katrenko, Willem van Hage, Konstantinos Krommydas, Pieter W Adriaans
2009 BMC Bioinformatics  
Semantic Web technologies are used to structure and store knowledge, while a workflow extracts knowledge from text.  ...  Semantic Web provides tools for sharing prior knowledge, while information retrieval and information extraction techniques enable its extraction from literature.  ...  Special thanks go to Bob Hertzberger who made the VL-e project a reality.  ... 
doi:10.1186/1471-2105-10-s10-s9 pmid:19796406 pmcid:PMC2755830 fatcat:hf7i72w2uzbm5mnzlqw774x4je

D2.1: Supply Chain Analysis and Requirements

Julien Mascolo Jlenia Puma, Eleni-Maria Kalogeraki Sofoklis Efremidis, Danijela Boberic Krsticev, Nineta Polemi Alexandra Michota, Nikos Argyropoulos, Manolis Chatzimpyrros, Haralambos Mouratidis, Gregory Chrysos, Farhan Sahito, Pablo Giménez Salazar, Norma Zanetti, Sophia Karagiorgou
2021 Zenodo  
The first one gives information on a glossary that forms the basis of the concepts used in the project, while the second one gives details regarding the first workshop organized with the Advisory Boards  ...  (e) The PCS has a web application deployed on a web server IIS 10. This allows access to all information and documents available and provide the necessary documents.  ...  (e) The PCS has a web application deployed on a web server IIS 10. This allows access to all information and documents available and provide the necessary documents.  ... 
doi:10.5281/zenodo.4884936 fatcat:67d3zmi7efhrzowbjleggzktgq

Extracting semantically enriched events from biomedical literature

Makoto Miwa, Paul Thompson, John McNaught, Douglas B Kell, Sophia Ananiadou
2012 BMC Bioinformatics  
Results: Based on a corpus of 1,000 MEDLINE abstracts, fully manually annotated with both events and associated meta-knowledge, we have constructed a machine learning-based system that automatically assigns  ...  However, existing event-based systems typically ignore additional information within the textual context of events that can determine, amongst other things, whether an event represents a fact, hypothesis  ...  We constructed a UIMA component for our EventMine-MK system (also available as a UIMAcompatible web service), which takes as input a sentence with NE annotation and outputs events contained within the  ... 
doi:10.1186/1471-2105-13-108 pmid:22621266 pmcid:PMC3464657 fatcat:fpxrrl7ukjekbjjpgqwtg6ocbe
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