{ "cells": [ { "cell_type": "markdown", "id": "dd40dae7", "metadata": { "papermill": { "duration": 0.009925, "end_time": "2024-07-01T13:29:06.198988", "exception": false, "start_time": "2024-07-01T13:29:06.189063", "status": "completed" }, "tags": [] }, "source": [ "# Metadata table" ] }, { "cell_type": "code", "execution_count": 1, "id": "4b2375cc", "metadata": { "execution": { "iopub.execute_input": "2024-07-01T13:29:06.212284Z", "iopub.status.busy": "2024-07-01T13:29:06.211862Z", "iopub.status.idle": "2024-07-01T13:29:06.223293Z", "shell.execute_reply": "2024-07-01T13:29:06.222654Z" }, "papermill": { "duration": 0.020696, "end_time": "2024-07-01T13:29:06.225351", "exception": false, "start_time": "2024-07-01T13:29:06.204655", "status": "completed" }, "tags": [ "remove-input" ] }, "outputs": [], "source": [ "# NO CODE\n", "from json2html import json2html\n", "import json, re\n", "from IPython.display import HTML" ] }, { "cell_type": "code", "execution_count": 2, "id": "3c5181cf", "metadata": { "execution": { "iopub.execute_input": "2024-07-01T13:29:06.238028Z", "iopub.status.busy": "2024-07-01T13:29:06.237803Z", "iopub.status.idle": "2024-07-01T13:29:06.241648Z", "shell.execute_reply": "2024-07-01T13:29:06.240845Z" }, "papermill": { "duration": 0.012884, "end_time": "2024-07-01T13:29:06.244151", "exception": false, "start_time": "2024-07-01T13:29:06.231267", "status": "completed" }, "tags": [ "parameters", "remove-input" ] }, "outputs": [], "source": [ "# NO CODE\n", "# PARAMETERS\n", "path = './meta/environment/meteocat_xema'" ] }, { "cell_type": "code", "execution_count": 3, "id": "3952fc5f", "metadata": { "execution": { "iopub.execute_input": "2024-07-01T13:29:06.258080Z", "iopub.status.busy": "2024-07-01T13:29:06.257541Z", "iopub.status.idle": "2024-07-01T13:29:06.261285Z", "shell.execute_reply": "2024-07-01T13:29:06.260533Z" }, "papermill": { "duration": 0.013641, "end_time": "2024-07-01T13:29:06.263537", "exception": false, "start_time": "2024-07-01T13:29:06.249896", "status": "completed" }, "tags": [ "injected-parameters" ] }, "outputs": [], "source": [ "# Parameters\n", "path = \"./meta/mosquito_alert/analytic_tables\"\n" ] }, { "cell_type": "code", "execution_count": 4, "id": "ca97677b", "metadata": { "execution": { "iopub.execute_input": "2024-07-01T13:29:06.278589Z", "iopub.status.busy": "2024-07-01T13:29:06.278266Z", "iopub.status.idle": "2024-07-01T13:29:06.302597Z", "shell.execute_reply": "2024-07-01T13:29:06.301816Z" }, "papermill": { "duration": 0.034669, "end_time": "2024-07-01T13:29:06.304771", "exception": false, "start_time": "2024-07-01T13:29:06.270102", "status": "completed" }, "tags": [ "remove-input", "full-width" ] }, "outputs": [ { "data": { "text/html": [ "
$schema../schema.json
@context
@vocabhttps://schema.org/
qudthttp://qudt.org/schema/qudt/
xsdhttp://www.w3.org/2001/XMLSchema#
@typeDataCatalog
nameanalytic_tables
conditionsOfAccessPrivate
descriptionTables from Mosquito Alert database (TigaData) selected for analytic purposes. Export from database is performed daily. Access to data is possible within ftp authentication to the host webserver.mosquitoalert.com
licenseAll rights reserved
citation
  • Eritja, R., Palmer, J. R. B., Roiz, D., Sanpera-Calbet, I., and Bartumeus, F., “Direct Evidence of Adult Aedes albopictus Dispersal by Car”, Scientific Reports, vol. 7, 2017. doi:10.1038/s41598-017-12652-5
  • Palmer, J. R. B., “Citizen science provides a reliable and scalable tool to track disease-carrying mosquitoes”, Nature Communications, vol. 8, 2017. doi:10.1038/s41467-017-00914-9
temporalCoverage2014-05-27/..
spatialCoverage
@typePlace
nameWorldwide
sameAshttps://www.wikidata.org/wiki/Q13780930
hasPart
  • @typeDataset
    nametigaserver_app_tigauser
    descriptionStores all user's Mosquito Alert application scores and some general information about the users
    distribution
    • @typeDataDownload
      namemosquitoalert_webserver_sftp
      descriptionDistribution by SFTP protocol from MosquitoAlert webserver.
      encodingFormatCSV
      workExample./notebooks/analytic_tables.py
      contentUrl
      • sftp://epidata@webserver.mosquitoalert.com:9122/tmp/tigaserver_app_tigauser.csv
      contentSize~10MB
    variableMeasured
    • @typePropertyValue
      nameuser_UUID
      descriptionHash that replaces a user name
      qudt:dataTypexsd:string
    • @typePropertyValue
      nameregistration_time
      descriptionRegistration time of the user (app installation time and registration)
      qudt:dataTypexsd:dateTime
    • @typePropertyValue
      namedevice_token
      descriptionDevice api-token key
      qudt:dataTypexsd:string
    • @typePropertyValue
      namescore
      descriptionScore of the user gained by submitting Mosquito Alert reports
      qudt:dataTypexsd:int
    • @typePropertyValue
      nameprofile_id
      description
      qudt:dataTypexsd:int
    • @typePropertyValue
      namescore_v2
      descriptionOverall score (version 2)
      qudt:dataTypexsd:int
    • @typePropertyValue
      namescore_v2_adult
      descriptionAdult mosquito score
      qudt:dataTypexsd:int
    • @typePropertyValue
      namescore_v2_bite
      descriptionMosquito bite score
      qudt:dataTypexsd:int
    • @typePropertyValue
      namescore_v2_site
      descriptionBreeding site score
      qudt:dataTypexsd:int
  • @typeDataset
    nametigaserver_app_report
    descriptionRegister of Mosquito Alert reports made by users at a given time and location with a given mobile device. Only the report ID is stored and not the whole report data content.
    distribution
    • @typeDataDownload
      namemosquitoalert_webserver_sftp
      descriptionDistribution by SFTP protocol from MosquitoAlert webserver.
      encodingFormatCSV
      workExample./notebooks/analytic_tables.py
      contentUrl
      • sftp://epidata@webserver.mosquitoalert.com:9122/tmp/tigaserver_app_report.csv
      contentSize~14MB
    variableMeasured
    • @typePropertyValue
      nameversion_UUID
      descriptionUUID randomly generated on phone to identify each unique report version. Must be exactly 36 characters (32 hex digits plus4 hyphens). Example: D18007F8-FD36-4288-8876-E4314A7B86AA
      qudt:dataTypexsd:string
    • @typePropertyValue
      nameversion_number
      descriptionVersion number of a report
      qudt:dataTypexsd:int
    • @typePropertyValue
      nameuser_id
      descriptionUser ID of the citizen scientist participant
      qudt:dataTypexsd:string
    • @typePropertyValue
      namereport_id
      descriptionNot unique report identifier that refers to a report independently of a given version.
      qudt:dataTypexsd:string
    • @typePropertyValue
      nameserver_upload_time
      descriptionTimestamp relative to the upload of the report to the server
      qudt:dataTypexsd:dateTime
    • @typePropertyValue
      namephone_upload_time
      descriptionTimestamp relative to the upload of the report to the mobile-app
      qudt:dataTypexsd:dateTime
    • @typePropertyValue
      namecreation_time
      descriptionDate and time on phone when first version of report was created. Format as [ECMA 262](http://ecma-international.org/ecma-262/5.1/#sec-15.9.1.15) date time string. Example: 2016-01-03T12:04:00.996Z
      qudt:dataTypexsd:dateTime
    • @typePropertyValue
      nameversion_time
      descriptionDate and time on phone when a given version of report was created. Format as [ECMA 262](http://ecma-international.org/ecma-262/5.1/#sec-15.9.1.15) date time string. Example: 2016-01-03T12:04:00.996Z
      qudt:dataTypexsd:dateTime
    • @typePropertyValue
      nametype
      descriptionType of report: 'adult', 'site', 'mission' or 'bite'
      qudt:dataTypexsd:string
    • @typePropertyValue
      namemission_id
      descriptionIdentifier of the mission relative to the 'tigaserver_app_mission' table
      qudt:dataTypexsd:int
    • @typePropertyValue
      namelocation_choice
      descriptionGeoreference location choice: 'current', 'selected', 'missing'.
      qudt:dataTypexsd:string
    • @typePropertyValue
      namecurrent_location_lon
      descriptionLongitude coordinate relative to the current location
      qudt:dataTypexsd:float
    • @typePropertyValue
      namecurrent_location_lat
      descriptionLatitude coordinate relative to the current location
      qudt:dataTypexsd:float
    • @typePropertyValue
      nameselected_location_lon
      descriptionLongitude coordinate relative to the selected location
      qudt:dataTypexsd:float
    • @typePropertyValue
      nameselected_location_lat
      descriptionLatitude coordinate relative to the selected location
      qudt:dataTypexsd:float
    • @typePropertyValue
      namenote
      descriptionNotes attached by the user that has sent the report
      qudt:dataTypexsd:string
    • @typePropertyValue
      namepackage_name
      descriptionMobile-app package name
      qudt:dataTypexsd:string
    • @typePropertyValue
      namepackage_version
      descriptionMobile-app package version
      qudt:dataTypexsd:int
    • @typePropertyValue
      namedevice_manufacturer
      descriptionUser mobile device manufacturer
      qudt:dataTypexsd:string
    • @typePropertyValue
      namedevice_model
      descriptionUser mobile device model
      qudt:dataTypexsd:string
    • @typePropertyValue
      nameos
      descriptionUser mobile device operation system
      qudt:dataTypexsd:string
    • @typePropertyValue
      nameos_version
      descriptionUser mobile device operation system version
      qudt:dataTypexsd:string
    • @typePropertyValue
      nameos_language
      descriptionUser mobile device operation system language
      qudt:dataTypexsd:string
    • @typePropertyValue
      nameapp_language
      descriptionLanguage of the mobile-app installed on the user mobile device
      qudt:dataTypexsd:string
    • @typePropertyValue
      namehide
      descriptionReport hidden from the public view because of unappropriated or not relevant content.
      qudt:dataTypexsd:boolean
    • @typePropertyValue
      namepoint
      descriptionCoordinate point lat/lon values with the relative Spatial Reference System Identifier (SRID) with Well-Known Binary (WKB) representation of the geometry.
      qudt:dataTypexsd:string
    • @typePropertyValue
      namecached_visible
      descriptionDecides if the report should be displayed on the web-map
      qudt:dataTypexsd:int
    • @typePropertyValue
      namecountry_id
      descriptionEuropean country identifier relative to the 'europe_countries' table
      qudt:dataTypexsd:int
    • @typePropertyValue
      namesession_id
      description
      qudt:dataTypexsd:int
    • @typePropertyValue
      namenuts_3
      descriptionNUTS level 3
      qudt:dataTypexsd:string
    • @typePropertyValue
      namenuts_2
      descriptionNUTS level 2
      qudt:dataTypexsd:string
    • @typePropertyValue
      nameia_filter_1
      descriptionArtificial Intelligence filter for Insect/noInsect classification (isInsect). Class score values are normalized on a range between -1 and 1 (e.g. -1 indicate not an insect and +1 indicate an insect).
      qudt:dataTypexsd:float
    • @typePropertyValue
      nameia_filter_2
      descriptionArtificial Intelligence filter for mosquito species classification (fSpecies). Negative values indicate relative score under the threshold (weak species identification confidence); positive values indicate relative score above the threshold (strong identification confidence); if report has no images returns -2; if report has no nuts3 info returns -3.
      qudt:dataTypexsd:float
  • @typeDataset
    nametigaserver_app_fix
    descriptionSampling effort measurement given by Mosquito Alert users location
    distribution
    • @typeDataDownload
      namemosquitoalert_webserver_sftp
      descriptionDistribution by SFTP protocol from MosquitoAlert webserver.
      encodingFormatCSV
      workExample./notebooks/analytic_tables.py
      contentUrl
      • sftp://epidata@webserver.mosquitoalert.com:9122/tmp/tigaserver_app_fix.csv
      contentSize~160MB
    variableMeasured
    • @typePropertyValue
      nameid
      descriptionIncremental unique identifier
      qudt:dataTypexsd:int
    • @typePropertyValue
      namefix_time
      description
      qudt:dataTypexsd:dateTime
    • @typePropertyValue
      nameserver_upload_time
      description
      qudt:dataTypexsd:dateTime
    • @typePropertyValue
      namephone_upload_time
      description
      qudt:dataTypexsd:dateTime
    • @typePropertyValue
      namemasked_lon
      description
      qudt:dataTypexsd:float
    • @typePropertyValue
      namemasked_lat
      description
      qudt:dataTypexsd:float
    • @typePropertyValue
      namepower
      description
      qudt:dataTypexsd:float
    • @typePropertyValue
      nameuser_coverage_uuid
      description
      qudt:dataTypexsd:string
    • @typePropertyValue
      namemask_size
      description
      qudt:dataTypexsd:string
  • @typeDataset
    nametigaserver_app_photo
    descriptionIdentifier references to Mosquito Alert report pictures
    distribution
    • @typeDataDownload
      namemosquitoalert_webserver_sftp
      descriptionDistribution by SFTP protocol from MosquitoAlert webserver.
      encodingFormatCSV
      workExample./notebooks/analytic_tables.py
      contentUrl
      • sftp://epidata@webserver.mosquitoalert.com:9122/tmp/tigaserver_app_photo.csv
      contentSize~6MB
    variableMeasured
    • @typePropertyValue
      nameid
      descriptionIdentifier of a picture
      qudt:dataTypexsd:int
    • @typePropertyValue
      namephoto
      descriptionUrl path to be added to http://webserver.mosquitoalert.com//media in order to get a picture
      qudt:dataTypexsd:string
    • @typePropertyValue
      namereport_id
      descriptionReport identifier to which a picture is associated
      qudt:dataTypexsd:string
    • @typePropertyValue
      namehide
      descriptionHidden or viewable picture
      qudt:dataTypexsd:boolean
    • @typePropertyValue
      nameuuid
      descriptionHashed unique identifier of a picture
      qudt:dataTypexsd:string
    • @typePropertyValue
      nameblood_genre
      descriptionVisual description of the mosquito possible states: 'female', 'fblood' (female with blood), 'dk' (don't know), 'fgblood' (female gravid with blood), 'fgravid' (female gravid), 'male'
      qudt:dataTypexsd:string
  • @typeDataset
    nametigacrafting_expertreportannotation
    descriptionEntomology experts results relative to each report
    distribution
    • @typeDataDownload
      namemosquitoalert_webserver_sftp
      descriptionDistribution by SFTP protocol from MosquitoAlert webserver.
      encodingFormatCSV
      workExample./notebooks/analytic_tables.py
      contentUrl
      • sftp://epidata@webserver.mosquitoalert.com:9122/tmp/tigacrafting_expertreportannotation.csv
      contentSize~53MB
    variableMeasured
    • @typePropertyValue
      nameid
      descriptionUnique identifier of a classification instance
      qudt:dataTypexsd:int
    • @typePropertyValue
      nameuser_id
      descriptionEntomology expert user ID
      qudt:dataTypexsd:int
    • @typePropertyValue
      namereport_id
      descriptionReport identifier to which an expert's validation is associated
      qudt:dataTypexsd:string
    • @typePropertyValue
      nametiger_certainty_category
      descriptionTiger mosquito certainty categories: '-2' definitely not a tiger mosquito; '-1' probably not a tiger mosquito; '0' not sure; '1' probably a tiger mosquito; '2' definitely a tiger mosquito.
      qudt:dataTypexsd:int
    • @typePropertyValue
      nametiger_certainty_notes
      descriptionTiger mosquito certainty notes
      qudt:dataTypexsd:string
    • @typePropertyValue
      namesite_certainty_category
      descriptionBreeding site certainty categories: '2' definitely a breeding site; '1' probably a breeding site; '0' not sure'; '-1' probably not a breeding site; '-2' definitely not a breeding site.
      qudt:dataTypexsd:int
    • @typePropertyValue
      namesite_certainty_notes
      descriptionBreeding site certainty notes
      qudt:dataTypexsd:string
    • @typePropertyValue
      nameedited_user_notes
      descriptionNotes written by validation experts (or written by the participant who sent the report and then edited by validation experts) for display on pubic map.
      qudt:dataTypexsd:string
    • @typePropertyValue
      namelast_modified
      descriptionTimestamp of report's last modification (update) performed by a given expert.
      qudt:dataTypexsd:dateTime
    • @typePropertyValue
      namecreated
      descriptionTimestamp of when a report was assigned to an expert in order to be validated.
      qudt:dataTypexsd:dateTime
    • @typePropertyValue
      namevalidation_complete
      descriptionCheckmark if the expert completed the validation task
      qudt:dataTypexsd:boolean
    • @typePropertyValue
      namebest_photo_id
      descriptionUnique identifier of the best photo assigned by the expert
      qudt:dataTypexsd:int
    • @typePropertyValue
      namelinked_id
      descriptionNotes used internally by the entomology experts community.
      qudt:dataTypexsd:string
    • @typePropertyValue
      namemessage_for_user
      descriptionMessage of the expert returned to the participant that submitted the report
      qudt:dataTypexsd:string
    • @typePropertyValue
      namestatus
      descriptionStatus given by the expert to an assigned report: '1' public; '0' flagged; '-1' hidden
      qudt:dataTypexsd:int
    • @typePropertyValue
      namerevise
      descriptionIndicates that the super-expert has revised the annotations of the experts. The majority voting algorithm result is discarded in favor of super-expert's opinion.
      qudt:dataTypexsd:boolean
    • @typePropertyValue
      nameaegypti_certainty_category
      descriptionAegypti mosquito certainty categories: '-2' definitely not an aegypti; '-1' probably not an aegypti; '0' not sure; '1' probably an aegypti; '2' definitely an aegypti.
      qudt:dataTypexsd:int
    • @typePropertyValue
      namesimplified_annotation
      descriptionIndicates if the expert annotation is of simple type. Only the last expert that validates a report indicate the best-photo and replies to the user, while the first experts only perform a simplified annotation.
      qudt:dataTypexsd:boolean
    • @typePropertyValue
      namecategory_id
      descriptionMosquito species category identifier related to the 'tigacrafting_categories' table
      qudt:dataTypexsd:int
    • @typePropertyValue
      namecomplex_id
      descriptionMosquito complex species category: '1' japonicus/koreicus; '2' albopictus/cretinus
      qudt:dataTypexsd:int
    • @typePropertyValue
      namevalidation_value
      descriptionCertainty associated with a species classification: '1' probable; '2' sure; '0' none. This attribute replace the old '*_certainty_category' categories.
      qudt:dataTypexsd:int
    • @typePropertyValue
      nameother_species_id
      descriptionOther species identifier (103 EU-species)
      qudt:dataTypexsd:int
    • @typePropertyValue
      namevalidation_complete_executive
      descriptionIf true, the report was reviewed by the super-expert and the opinion of other experts was not considered
      qudt:dataTypexsd:boolean
  • @typeDataset
    nametigaserver_app_reportresponse
    descriptionResponses of participants relative to a report.
    distribution
    • @typeDataDownload
      namemosquitoalert_webserver_sftp
      descriptionDistribution by SFTP protocol from MosquitoAlert webserver.
      encodingFormatCSV
      workExample./notebooks/analytic_tables.py
      contentUrl
      • sftp://epidata@webserver.mosquitoalert.com:9122/tmp/tigaserver_app_reportresponse.csv
      contentSize~36MB
    variableMeasured
    • @typePropertyValue
      nameid
      descriptionIdentifier of the participant response
      qudt:dataTypexsd:int
    • @typePropertyValue
      namereport_id
      descriptionIdentifier of the report
      qudt:dataTypexsd:string
    • @typePropertyValue
      namequestion
      descriptionText format question in default language. Language translations are available on the mobile-app 'translation_dict' table.
      qudt:dataTypexsd:string
    • @typePropertyValue
      nameanswer
      descriptionText format answer in default language. Language translations are available on the mobile-app 'translation_dict' table.
      qudt:dataTypexsd:string
    • @typePropertyValue
      nameanswer_id
      descriptionAnswer identifier
      qudt:dataTypexsd:int
    • @typePropertyValue
      nameanswer_value
      descriptionValue relative to the answer
      qudt:dataTypexsd:int
    • @typePropertyValue
      namequestion_id
      descriptionquestion identifier
      qudt:dataTypexsd:int
measurementTechnique
  • Mobile application for citizen science
  • Data validation by entomologists
creator
  • @typeProject
    @idMA
    nameMosquito Alert, Proyecto Coordinado por CREAF, CEAB-CSIC e ICREA
    contactPoint
    @typeContactPoint
    emailinfo@mosquitoalert.com
    urlhttp://www.mosquitoalert.com/
  • @typePerson
    @idJP
    namePalmer, John Rossman Bertholf
    identifierhttps://orcid.org/0000-0002-2648-7860
    contactPoint
    @typeContactPoint
    contactTypeprincipal investigator
    emailjohn.palmer@upf.edu
    urlhttps://www.upf.edu/web/gritim/entry/-/-/50722/adscripcion/john-rossman-bertholf-palmer/
  • @typePerson
    @idAE
    nameEscobar Rúbies, Agustí
    identifierhttps://orcid.org/0000-0002-6856-0480
    contactPoint
    @typeContactPoint
    contactTypeprogrammer
    emaila.escobar@creaf.uab.es
    urlhttp://www.creaf.cat/es/personal/agusti-escobar-rubies/
" ], "text/plain": [ "" ] }, "execution_count": 4, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# NO CODE\n", "# FULL WIDTH\n", "with open(f'{path}.json') as f:\n", " data = json.load(f)\n", "\n", "table = json2html.convert(json=data, clubbing=False)\n", "table_sub = re.sub('', '', table)\n", "\n", "HTML(table_sub)\n", "\n", "# Run the following in the command line to build a html table\n", "# $ jupyter nbconvert --to html --no-input --no-prompt build_tables.ipynb\n" ] }, { "cell_type": "code", "execution_count": null, "id": "467d22d2", "metadata": { "papermill": { "duration": 0.007299, "end_time": "2024-07-01T13:29:06.319485", "exception": false, "start_time": "2024-07-01T13:29:06.312186", "status": "completed" }, "tags": [] }, "outputs": [], "source": [] } ], "metadata": { "interpreter": { "hash": "524d3359b179f3b444361f48db8ae048bd8c237924fac1cd48a4c6f8144f6452" }, "kernelspec": { "display_name": "Python 3.7.10 64-bit ('scidb': conda)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.10.4" }, "metadata": { "interpreter": { "hash": "e3961729dbf4ff77740ff872c9a3eef08621b5b434e3d8d81026af4505918c74" } }, "papermill": { "default_parameters": {}, "duration": 2.338722, "end_time": "2024-07-01T13:29:06.648275", "environment_variables": {}, "exception": null, "input_path": "build_info.ipynb", "output_path": "./meta_ipynb/analytic_tables.ipynb", "parameters": { "path": "./meta/mosquito_alert/analytic_tables" }, "start_time": "2024-07-01T13:29:04.309553", "version": "2.3.4" } }, "nbformat": 4, "nbformat_minor": 5 }