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A web application to unlock primary biodiversity data from published literature

Home Page: https://fgabriel1891.github.io/BiodiversityObservationsMiner/

License: MIT License

R 1.96% HTML 98.04% CSS 0.01%

biodiversity biodiversity-data mining literature shiny

biodiversityobservationsminer's Introduction

Biodiversity Observations Miner

A web application to unlock primary biodiversity data from published literature

Running the application

To run locally on your computer:

1.- Fork or download the repository to a directory on your computer

2.- Open the R Project container file

3.- Make sure you have all R packages installed and updated to run the app (see below)

4.- Run the app with RStudio.

Alternatively, you can run the shiny::runGitHub() function. Function arguments: repo= "BiodiversityObservationsMiner", username= "fgabriel1891".

Important! Before using Biodiversity Observations Miner locally we recommend to have R and Rstudio installed and up to date.

For comments, suggestions and bugs please open an issue

About

The idea to develop this web application is set in the context of increasing the digital mobility and interoperability of biodiversity data wordwide. I developed Biodiversity Observations Miner with guidance and input from W. Daniel Kissling and Emiel van Loon of the Institute of Biodiversity and Ecosystems Dynamics (IBED) from the University of Amsterdam (UvA).

R packages required

Acknowledgements

Biodiversity Observations Miner uses tools from the GlobalNamesArchitecture (GNA) implemented in the taxize package. Thanks to Scott Chamberlain for modifications to taxize that improved the functionality of this application. Credits to the developers of the individual packages that Biodiversity Observations Miner is dependent on. Terms composing the pollination biodiversity dictionary were selected in collaboration with Joan Casanelles.

biodiversityobservationsminer's People

Contributors

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komax kephelps pakillo kkougiou antecede invasive-mammal-dynamics a-stupid-fish

biodiversityobservationsminer's Issues

Error to get taxa - BOM

Dear Gabriel Muñoz,

I’m trying to explore the Biodiversity Observations Miner, but when I got the message “Error: An error has occurred. Check your logs or contact the app author for clarification”. I have been tried using chrome and edge and, also tried to find data by taxonomic name and key-words.

The results were always the same. Could you help me with the use of the app?

I’m very interested to use BOM to get plant records from urban areas datasets. Would be possible to use BOM to get this kind of data? If no, do you have any suggestions?

Thank you very much.

Best regards,
Gustavo
[email protected]

Error when i run BOM locally

I installed BOM locally on my pc as suggested in the manual and it starts just fine. When i upload files and press the get taxa button i get a message "error: 'names' attribute [2] must be the same length as the vector [1]". I tried changing the file names and even reinstalled the packages but i get the same result. Any suggestion of how can i fix that?

XMLHttpRequest error

Really neat project and associated paper. On your hosted site, I'm getting this error message in the console ...

[Deprecation] Synchronous XMLHttpRequest on the main thread is deprecated because of its detrimental effects to the end user's experience. For more help, check https://xhr.spec.whatwg.org/. send @ jquery.min.js:4

... along with some notices in the UI after hitting the "Get Taxa" button.

Cheers!

Warning: Error in hasGroups: object 'path2' not found

Dear Gabriel Muñoz,

I’m trying to locally construct the Biodiversity Observations Miner, but I got the message Warning: Error in hasGroups: object 'path2' not found. In BiodiversityObservationsMiner - master path to run runApp (), I can get the right results in by taxa page, when I want to go to the by keywords further screening data, click on the Use a biodiversity dictionary to filter results (optional) checkbox will error (mentioned above). I see that the dic path is defined in the ui.R script and is a relative path, which should be fine.

Even if Rstudio was restarted, the result was always the same. Could you help me with the use of the locally app?

Your project is very interesting and very promising! Thank you for creating and open-source such a project! If possible, I also look forward to cooperating with you!

Thank you very much.

Best regards,
Bing
[email protected]

how to debug locally error ?

runApp()

Listening on http://127.0.0.1:4109
Warning in readLines(con) :
incomplete final line found on 'www/settings.Rmd'
Warning in readLines(con) :
incomplete final line found on 'www/02-About.Rmd'
Warning: Error in sub: input string 1 is invalid UTF-8
[No stack trace available]

sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936
[2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936
[3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936
[4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_People's Republic of China.936

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] shinydashboard_0.7.1 shinythemes_1.1.1 shiny_1.2.0

loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 crayon_1.3.4 packrat_0.5.0 digest_0.6.18 later_0.7.5 mime_0.6 R6_2.3.0
[8] xtable_1.8-3 magrittr_1.5 rstudioapi_0.8 promises_1.0.1 DT_0.5 tools_3.5.1 htmlwidgets_1.3
[15] markdown_0.9 crosstalk_1.0.0 yaml_2.2.0 httpuv_1.4.5 rsconnect_0.8.12 compiler_3.5.1 htmltools_0.3.6