Pub Date : 2018-09-15DOI: 10.7287/peerj.preprints.27210v1
J. A. Ribeiro, J. L. N. E. S. Brito, Orlando Bernardo Filho, I. Badolato, Rodrigo Dacome, G. Mota
This paper shows our experience at the Rio de Janeiro State University (UERJ), in Brazil, developing and using the E-Foto software, one of the main achievements of the E-Foto project that aims to built-up a software tool for teaching digital photogrammetry and software development, to both graduate and undergraduate students, in the fields of Cartographic and Computer Engineering. E-Foto main objective is to diminish the gap that exists nowadays between the teaching of Photogrammetry and Remote Sensing in universities and Research Institutions of developing countries and the high-tech expensive systems that are used under the production environment.
{"title":"E-Foto: an educational photogrammetric workstation","authors":"J. A. Ribeiro, J. L. N. E. S. Brito, Orlando Bernardo Filho, I. Badolato, Rodrigo Dacome, G. Mota","doi":"10.7287/peerj.preprints.27210v1","DOIUrl":"https://doi.org/10.7287/peerj.preprints.27210v1","url":null,"abstract":"This paper shows our experience at the Rio de Janeiro State University (UERJ), in Brazil, developing and using the E-Foto software, one of the main achievements of the E-Foto project that aims to built-up a software tool for teaching digital photogrammetry and software development, to both graduate and undergraduate students, in the fields of Cartographic and Computer Engineering.\u0000 E-Foto main objective is to diminish the gap that exists nowadays between the teaching of Photogrammetry and Remote Sensing in universities and Research Institutions of developing countries and the high-tech expensive systems that are used under the production environment.","PeriodicalId":93040,"journal":{"name":"PeerJ preprints","volume":"104 1","pages":"e27210"},"PeriodicalIF":0.0,"publicationDate":"2018-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81761874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-09-14DOI: 10.7287/peerj.preprints.27208v1
N. Long, T. Gardes, J. Hidalgo, V. Masson, Robert Schoetter
This article presents the development and application to a set of French urban agglomerations of a method for Local Climate Zones (LCZ) attribution using the open-source language R. The LCZs classify the urban fabric at high spatial scale (such as a block of houses) according to its morphological characteristicsand land use. The LCZ classification is carried out for 42 urban agglomerations and is then related to urban heat island intensity (UHII) obtained from numerical simulations at a spatial resolution of 250m. The objective is to study the adequacy of the LCZ classification to characterise the impact of urban morphology on the UHII. The variance analysis (ANOVA) carried out confirms the highly significant relationship between LCZs and the UHII for a given urban agglomeration. For all the urban agglomerations in the sample, linear regression models show a significant correlation between the percentages of surface covered by different LCZ and the mean UHII for the time periods tested (21-23 UTC), with adjusted coefficients of determination higher than 0.40.
{"title":"Influence of the urban morphology on the urban heat island intensity: an approach based on the Local Climate Zone classification","authors":"N. Long, T. Gardes, J. Hidalgo, V. Masson, Robert Schoetter","doi":"10.7287/peerj.preprints.27208v1","DOIUrl":"https://doi.org/10.7287/peerj.preprints.27208v1","url":null,"abstract":"This article presents the development and application to a set of French urban agglomerations of a method for Local Climate Zones (LCZ) attribution using the open-source language R. The LCZs classify the urban fabric at high spatial scale (such as a block of houses) according to its morphological characteristicsand land use. The LCZ classification is carried out for 42 urban agglomerations and is then related to urban heat island intensity (UHII) obtained from numerical simulations at a spatial resolution of 250m. The objective is to study the adequacy of the LCZ classification to characterise the impact of urban morphology on the UHII. The variance analysis (ANOVA) carried out confirms the highly significant relationship between LCZs and the UHII for a given urban agglomeration. For all the urban agglomerations in the sample, linear regression models show a significant correlation between the percentages of surface covered by different LCZ and the mean UHII for the time periods tested (21-23 UTC), with adjusted coefficients of determination higher than 0.40.","PeriodicalId":93040,"journal":{"name":"PeerJ preprints","volume":"37 1","pages":"e27208"},"PeriodicalIF":0.0,"publicationDate":"2018-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73724954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-09-14DOI: 10.7287/peerj.preprints.27203v1
B. Köbben
At the ITC faculty of the University of Twente, we have been teaching cartography for more then 60 years. Throughout this period, the technology of mapping has undergone spectacular changes and nowadays most students do not draw their maps any more, but use software instead. However, for maps to be effective in communication, their design still has to follow the same rules as before. Ideally, one wants to teach these design rules independently from the tools, such that the students understand how a good map works, not just which buttons to click to create it. For this purpose, we created the Thematic Mapping Tutor. It is an open, web-based system that provides a structured way of constructing thematic maps out of selected data. The system uses the input of the student to construct a map in the Vega-Lite grammar, which is transformed to web-graphics. In this paper we describe the educational philosophy behind the system, as well as technical details about its functionality. We report on first tests, and reflect on the possibilities and pitfalls of the system.
{"title":"Open educational resources for cartography: the Thematic Mapping Tutor","authors":"B. Köbben","doi":"10.7287/peerj.preprints.27203v1","DOIUrl":"https://doi.org/10.7287/peerj.preprints.27203v1","url":null,"abstract":"At the ITC faculty of the University of Twente, we have been teaching cartography for more then 60 years. Throughout this period, the technology of mapping has undergone spectacular changes and nowadays most students do not draw their maps any more, but use software instead. However, for maps to be effective in communication, their design still has to follow the same rules as before. Ideally, one wants to teach these design rules independently from the tools, such that the students understand how a good map works, not just which buttons to click to create it.\u0000 For this purpose, we created the Thematic Mapping Tutor. It is an open, web-based system that provides a structured way of constructing thematic maps out of selected data. The system uses the input of the student to construct a map in the Vega-Lite grammar, which is transformed to web-graphics.\u0000 In this paper we describe the educational philosophy behind the system, as well as technical details about its functionality. We report on first tests, and reflect on the possibilities and pitfalls of the system.","PeriodicalId":93040,"journal":{"name":"PeerJ preprints","volume":"29 1","pages":"e27203"},"PeriodicalIF":0.0,"publicationDate":"2018-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87547613","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-09-14DOI: 10.7287/peerj.preprints.27204v1
N. Blanc, T. Produit, J. Ingensand
Smapshot is a web-based participatory virtual globe where users can georeference historical images of the landscape by clicking a minimum of six well identifiable correspondence points between the image and a 3D virtual globe. The images database is expected to grow exponentially. In a near future, the work of the web users will no longer be enough. To tackle this issue, we developed a semi-automatic process to georeference images. The volunteers will be shown only images having a maximum number of neighbour images in the matching graph. These neighbour images are the ones with which they share some overlay. This overlap is detected using the SIFT algorithm in a pairewise matching process. For an image pair made of a reference image with a known pose and a query image we want to georeference, we extracted the 3D world coordinates of the tie points from a digital elevation model. Then, by running a perspective-n-point algorithm after having geometrically tested the resulting homography between the two images, we compute the 6 degree of freedom pose, i.e. the position (X,Y,Z) and orientation (azimuth, tilt and roll angles) of the query image. The query image then becomes a reference and the georeference computation can be propagated more deeply in the graph structure.
{"title":"A semi-automatic tool to georeference historical landscape images","authors":"N. Blanc, T. Produit, J. Ingensand","doi":"10.7287/peerj.preprints.27204v1","DOIUrl":"https://doi.org/10.7287/peerj.preprints.27204v1","url":null,"abstract":"Smapshot is a web-based participatory virtual globe where users can georeference historical images of the landscape by clicking a minimum of six well identifiable correspondence points between the image and a 3D virtual globe. The images database is expected to grow exponentially. In a near future, the work of the web users will no longer be enough.\u0000 To tackle this issue, we developed a semi-automatic process to georeference images. The volunteers will be shown only images having a maximum number of neighbour images in the matching graph. These neighbour images are the ones with which they share some overlay. This overlap is detected using the SIFT algorithm in a pairewise matching process.\u0000 For an image pair made of a reference image with a known pose and a query image we want to georeference, we extracted the 3D world coordinates of the tie points from a digital elevation model.\u0000 Then, by running a perspective-n-point algorithm after having geometrically tested the resulting homography between the two images, we compute the 6 degree of freedom pose, i.e. the position (X,Y,Z) and orientation (azimuth, tilt and roll angles) of the query image. The query image then becomes a reference and the georeference computation can be propagated more deeply in the graph structure.","PeriodicalId":93040,"journal":{"name":"PeerJ preprints","volume":"44 1","pages":"e27204"},"PeriodicalIF":0.0,"publicationDate":"2018-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83226740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-09-14DOI: 10.7287/PEERJ.PREPRINTS.27206V1
P. Löwe, V. Petras, M. Neteler, H. Mitásová
The authors introduce the GRASS GIS add-on module g.citation. The module extends the existing citation capabilities of GRASS GIS, which until now only provide for automated citation of the software project as a whole, authored by the GRASS Development Team, without reference to individual persons. The functionalities of the new module enable individual code citation for each of the over 500 implemented functionalities, including add-on modules. Three different classes of citation output are provided in a variety human- and machine-readable formats. The implications of this reference implementation of scientific software citation for both for the GRASS GIS project and the OSGeo foundation are outlined.
{"title":"g.citation: Scientific citation for individual GRASS GIS software modules","authors":"P. Löwe, V. Petras, M. Neteler, H. Mitásová","doi":"10.7287/PEERJ.PREPRINTS.27206V1","DOIUrl":"https://doi.org/10.7287/PEERJ.PREPRINTS.27206V1","url":null,"abstract":"The authors introduce the GRASS GIS add-on module g.citation. The module extends the existing citation capabilities of GRASS GIS, which until now only provide for automated citation of the software project as a whole, authored by the GRASS Development Team, without reference to individual persons. The functionalities of the new module enable individual code citation for each of the over 500 implemented functionalities, including add-on modules. Three different classes of citation output are provided in a variety human- and machine-readable formats. The implications of this reference implementation of scientific software citation for both for the GRASS GIS project and the OSGeo foundation are outlined.","PeriodicalId":93040,"journal":{"name":"PeerJ preprints","volume":"442 1","pages":"e27206"},"PeriodicalIF":0.0,"publicationDate":"2018-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76465724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-09-14DOI: 10.7287/peerj.preprints.27207v1
T. Chassin, J. Ingensand, F. Joerin
This paper presents a platform aiming the ease of the debate between citizens. In the early 2010’ies, governments are seeking new ways to be more accountable and transparent towards their citizens; marking a renewal in public participation. In return, citizens are eager to be heard and to use new tools based on information and communication technologies (ICT) like the web 2.0. This public’s empowerment presents some costs for the authorities who are mainly concerned with the loss of decision making power. To face those challenges, several 2D online maps have been developed to help the governments to direct and centralize citizens insights. Those previous collaborating mapping tools helped to identify the characteristics of a reliable platform : user-friendly, simple and accessible (anywhere at any time). In our implementation, we adopted the third dimension which provides numerous benefits : 1. a more effective and effortless visualization, 2. An unbiased representation of the environment, 3. The merge of the participant cognition spaces. From our past experiences, we conceptualized the actors (citizens / facilitator / transcriber) interactions and dynamics in public engagement on-site meeting. From this approach, we evaluated how the utilization of a 3D virtual environment as the support of the participation will reshape and enhance the relation synergies between the actors : 1. Centralization of the interactions within the platform, 2. Automated analysis from the gathered raw information, 3. Reachability of a larger part of the population, 4. Lightening of the participatory processes.
{"title":"Towards an open 3D participatory citizen debate","authors":"T. Chassin, J. Ingensand, F. Joerin","doi":"10.7287/peerj.preprints.27207v1","DOIUrl":"https://doi.org/10.7287/peerj.preprints.27207v1","url":null,"abstract":"This paper presents a platform aiming the ease of the debate between citizens. In the early 2010’ies, governments are seeking new ways to be more accountable and transparent towards their citizens; marking a renewal in public participation. In return, citizens are eager to be heard and to use new tools based on information and communication technologies (ICT) like the web 2.0. This public’s empowerment presents some costs for the authorities who are mainly concerned with the loss of decision making power. To face those challenges, several 2D online maps have been developed to help the governments to direct and centralize citizens insights. Those previous collaborating mapping tools helped to identify the characteristics of a reliable platform : user-friendly, simple and accessible (anywhere at any time). In our implementation, we adopted the third dimension which provides numerous benefits : 1. a more effective and effortless visualization, 2. An unbiased representation of the environment, 3. The merge of the participant cognition spaces. From our past experiences, we conceptualized the actors (citizens / facilitator / transcriber) interactions and dynamics in public engagement on-site meeting. From this approach, we evaluated how the utilization of a 3D virtual environment as the support of the participation will reshape and enhance the relation synergies between the actors : 1. Centralization of the interactions within the platform, 2. Automated analysis from the gathered raw information, 3. Reachability of a larger part of the population, 4. Lightening of the participatory processes.","PeriodicalId":93040,"journal":{"name":"PeerJ preprints","volume":"132 1","pages":"e27207"},"PeriodicalIF":0.0,"publicationDate":"2018-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85744627","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-09-13DOI: 10.7287/peerj.preprints.27198v1
M. Lotfian, J. Ingensand, O. Ertz, Sarah Composto, M. Oberson, Simon Oulevay, D. Campisi, F. Joerin
The public participation in scientific projects (citizen science) is significantly increasing specially with technology developments in recent years. Volunteers play an essential role in citizen science projects, therefore understanding their motivations, and understanding how to sustain them to keep contributing to the project are of utmost importance. This paper presents the analysis of volunteers’ characteristics and their motivations to contribute to a citizen science project, which aims at encouraging citizens to take action for biodiversity. The results from the online survey illustrate that people are more motivated by intrinsic nature-related motives rather than extrinsic motivations.
{"title":"Participants' motivations to contribute to biodiversity citizen science projects","authors":"M. Lotfian, J. Ingensand, O. Ertz, Sarah Composto, M. Oberson, Simon Oulevay, D. Campisi, F. Joerin","doi":"10.7287/peerj.preprints.27198v1","DOIUrl":"https://doi.org/10.7287/peerj.preprints.27198v1","url":null,"abstract":"The public participation in scientific projects (citizen science) is significantly increasing specially with technology developments in recent years. Volunteers play an essential role in citizen science projects, therefore understanding their motivations, and understanding how to sustain them to keep contributing to the project are of utmost importance. This paper presents the analysis of volunteers’ characteristics and their motivations to contribute to a citizen science project, which aims at encouraging citizens to take action for biodiversity. The results from the online survey illustrate that people are more motivated by intrinsic nature-related motives rather than extrinsic motivations.","PeriodicalId":93040,"journal":{"name":"PeerJ preprints","volume":"106 1","pages":"e27198"},"PeriodicalIF":0.0,"publicationDate":"2018-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76139507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-09-11DOI: 10.7287/peerj.preprints.27189v1
M. Bessagnet, Patrick Etcheverry, Annig Lacayrelle, C. Marquesuzaà, Landy Rajaonarivo, P. Roose, A. Fonteles, C. Sallaberry
This paper presents part of the European FEDER Project TCVPYR, which aims to promote tourism in the French Pyrenees region by leveraging elements of its cultural heritage. The TCVPYR is a multidisciplinary project involving scientists from various domains, including: computers scientists, geographers, historians and anthropologists. In order to achieve its goal, some of the TCVPYR researchers are currently collecting georeferenced cultural heritage data in different areas of the Pyrenees. This data, together with data from the local governments and the Open Data, is intended to feed a mobile application that promotes the tourism in the region. The mobile application will allow tourists, but also scientists, to access cultural heritage data in the form of points of interest (POI). Moreover, these POI are to be presented according to the user profile and the environmental context, including spatiotemporal aspects such as his current location. For example, the application may suggest to a tourist an itinerary with several POI taking into account his interests, means of locomotion, available time and mobile features (battery level, internet connexion…). All data collected in this project as well as the final application will be published as open data and open source.
{"title":"Leveraging heterogeneous Cultural Heritage data to promote tourism","authors":"M. Bessagnet, Patrick Etcheverry, Annig Lacayrelle, C. Marquesuzaà, Landy Rajaonarivo, P. Roose, A. Fonteles, C. Sallaberry","doi":"10.7287/peerj.preprints.27189v1","DOIUrl":"https://doi.org/10.7287/peerj.preprints.27189v1","url":null,"abstract":"This paper presents part of the European FEDER Project TCVPYR, which aims to promote tourism in the French Pyrenees region by leveraging elements of its cultural heritage. The TCVPYR is a multidisciplinary project involving scientists from various domains, including: computers scientists, geographers, historians and anthropologists. In order to achieve its goal, some of the TCVPYR researchers are currently collecting georeferenced cultural heritage data in different areas of the Pyrenees. This data, together with data from the local governments and the Open Data, is intended to feed a mobile application that promotes the tourism in the region. The mobile application will allow tourists, but also scientists, to access cultural heritage data in the form of points of interest (POI). Moreover, these POI are to be presented according to the user profile and the environmental context, including spatiotemporal aspects such as his current location. For example, the application may suggest to a tourist an itinerary with several POI taking into account his interests, means of locomotion, available time and mobile features (battery level, internet connexion…). All data collected in this project as well as the final application will be published as open data and open source.","PeriodicalId":93040,"journal":{"name":"PeerJ preprints","volume":"30 1","pages":"e27189"},"PeriodicalIF":0.0,"publicationDate":"2018-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81338662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-08-29DOI: 10.7287/peerj.preprints.27159v1
Alvaro R. Ortiz Troncoso
Open source projects may face a forking situation at some point during their life-cycle. The traditional view is that forks are a waste of project resources and should be avoided. However, in a wider technological and organisational context, forks can be a way to foster the creation of a software ecosystem. Either way, forking is explicitly allowed by open source licenses. Notwithstanding, methods for quantifying the evolution of forks are currently scarce. The present work attempts to answer the question whether a real-life project has forked. It does so by considering code and organisational characteristics of the project, and analysing these characteristics by applying methods ported from biological phylogenetics. After finding that the project is forked, implications for project governance are discussed.
{"title":"Phylogenetic analysis of software evolution, a case study: VE&MINT","authors":"Alvaro R. Ortiz Troncoso","doi":"10.7287/peerj.preprints.27159v1","DOIUrl":"https://doi.org/10.7287/peerj.preprints.27159v1","url":null,"abstract":"Open source projects may face a forking situation at some point during their life-cycle. The traditional view is that forks are a waste of project resources and should be avoided. However, in a wider technological and organisational context, forks can be a way to foster the creation of a software ecosystem. Either way, forking is explicitly allowed by open source licenses. Notwithstanding, methods for quantifying the evolution of forks are currently scarce. The present work attempts to answer the question whether a real-life project has forked. It does so by considering code and organisational characteristics of the project, and analysing these characteristics by applying methods ported from biological phylogenetics. After finding that the project is forked, implications for project governance are discussed.","PeriodicalId":93040,"journal":{"name":"PeerJ preprints","volume":"53 1","pages":"e27159"},"PeriodicalIF":0.0,"publicationDate":"2018-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75310204","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-08-29DOI: 10.7287/peerj.preprints.27161v1
Morteza Pourreza Shahri, Madhusudan Srinivasan, D. Bimczok, Upulee Kanewala, Indika Kahanda
The Critical Assessment of protein Function Annotation algorithms (CAFA) is a large-scale experiment for assessing the computational models for automated function prediction (AFP). The models presented in CAFA have shown excellent promise in terms of prediction accuracy, but quality assurance has been paid relatively less attention. The main challenge associated with conducting systematic testing on AFP software is the lack of a test oracle, which determines passing or failing of a test case; unfortunately, the exact expected outcomes are not well defined for the AFP task. Thus, AFP tools face the oracle problem. Metamorphic testing (MT) is a technique used to test programs that face the oracle problem using metamorphic relations (MRs). A MR determines whether a test has passed or failed by specifying how the output should change according to a specific change made to the input. In this work, we use MT to test nine CAFA2 AFP tools by defining a set of MRs that apply input transformations at the protein-level. According to our initial testing, we observe that several tools fail all the test cases and two tools pass all the test cases on different GO ontologies.
{"title":"A look back at the quality of Protein Function Prediction tools in CAFA","authors":"Morteza Pourreza Shahri, Madhusudan Srinivasan, D. Bimczok, Upulee Kanewala, Indika Kahanda","doi":"10.7287/peerj.preprints.27161v1","DOIUrl":"https://doi.org/10.7287/peerj.preprints.27161v1","url":null,"abstract":"The Critical Assessment of protein Function Annotation algorithms (CAFA) is a large-scale experiment for assessing the computational models for automated function prediction (AFP). The models presented in CAFA have shown excellent promise in terms of prediction accuracy, but quality assurance has been paid relatively less attention. The main challenge associated with conducting systematic testing on AFP software is the lack of a test oracle, which determines passing or failing of a test case; unfortunately, the exact expected outcomes are not well defined for the AFP task. Thus, AFP tools face the oracle problem. Metamorphic testing (MT) is a technique used to test programs that face the oracle problem using metamorphic relations (MRs). A MR determines whether a test has passed or failed by specifying how the output should change according to a specific change made to the input. In this work, we use MT to test nine CAFA2 AFP tools by defining a set of MRs that apply input transformations at the protein-level. According to our initial testing, we observe that several tools fail all the test cases and two tools pass all the test cases on different GO ontologies.","PeriodicalId":93040,"journal":{"name":"PeerJ preprints","volume":"36 1","pages":"e27161"},"PeriodicalIF":0.0,"publicationDate":"2018-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82663765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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