{ "cells": [ { "cell_type": "markdown", "id": "4db697c2", "metadata": { "papermill": { "duration": 0.00908, "end_time": "2024-07-01T13:29:15.156617", "exception": false, "start_time": "2024-07-01T13:29:15.147537", "status": "completed" }, "tags": [] }, "source": [ "# Metadata table" ] }, { "cell_type": "code", "execution_count": 1, "id": "cda4e029", "metadata": { "execution": { "iopub.execute_input": "2024-07-01T13:29:15.169822Z", "iopub.status.busy": "2024-07-01T13:29:15.169041Z", "iopub.status.idle": "2024-07-01T13:29:15.184842Z", "shell.execute_reply": "2024-07-01T13:29:15.183418Z" }, "papermill": { "duration": 0.024992, "end_time": "2024-07-01T13:29:15.187328", "exception": false, "start_time": "2024-07-01T13:29:15.162336", "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": "901bf770", "metadata": { "execution": { "iopub.execute_input": "2024-07-01T13:29:15.204590Z", "iopub.status.busy": "2024-07-01T13:29:15.203941Z", "iopub.status.idle": "2024-07-01T13:29:15.210513Z", "shell.execute_reply": "2024-07-01T13:29:15.209645Z" }, "papermill": { "duration": 0.020882, "end_time": "2024-07-01T13:29:15.214124", "exception": false, "start_time": "2024-07-01T13:29:15.193242", "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": "849f21a7", "metadata": { "execution": { "iopub.execute_input": "2024-07-01T13:29:15.229757Z", "iopub.status.busy": "2024-07-01T13:29:15.229202Z", "iopub.status.idle": "2024-07-01T13:29:15.234837Z", "shell.execute_reply": "2024-07-01T13:29:15.234119Z" }, "papermill": { "duration": 0.014708, "end_time": "2024-07-01T13:29:15.236840", "exception": false, "start_time": "2024-07-01T13:29:15.222132", "status": "completed" }, "tags": [ "injected-parameters" ] }, "outputs": [], "source": [ "# Parameters\n", "path = \"./meta/mosquito_alert/reports\"\n" ] }, { "cell_type": "code", "execution_count": 4, "id": "89a20660", "metadata": { "execution": { "iopub.execute_input": "2024-07-01T13:29:15.252496Z", "iopub.status.busy": "2024-07-01T13:29:15.251895Z", "iopub.status.idle": "2024-07-01T13:29:15.274308Z", "shell.execute_reply": "2024-07-01T13:29:15.273228Z" }, "papermill": { "duration": 0.034866, "end_time": "2024-07-01T13:29:15.278452", "exception": false, "start_time": "2024-07-01T13:29:15.243586", "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#
@typeDataset
namereports
conditionsOfAccessPublic
descriptionThis dataset contains validated reports from the Mosquito Alert application, providing information on mosquito bites, breeding sites, and adult mosquito encounters.
urlhttps://github.com/MosquitoAlert/Data
licensehttps://creativecommons.org/publicdomain/zero/1.0/
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
distribution
  • @typeDataDownload
    namemosquitoalert_webserver_sftp
    descriptionDistribution by SFTP download from MosquitoAlert webserver
    encodingFormatJSON.ZIP
    workExample./notebooks/reports.py
    contentUrl
    • sftp://epidata@webserver.mosquitoalert.com:9122/home/webuser/webapps/Data/all_reports.zip
    contentSize46MB
  • @typeDataDownload
    namezenodo
    descriptionDistribution from Zenodo cloud.
    encodingFormat[JSON.ZIP].ZIP
    workExample./notebooks/reports.py
    contentUrl
    • https://doi.org/10.5281/zenodo.597466
    contentSize46MB
  • @typeDataDownload
    namemosquitoalert_github
    descriptionDistribution from MosquitoAlert Github repository
    encodingFormatJSON.ZIP
    workExample./notebooks/reports.py
    contentUrl
    • https://github.com/MosquitoAlert/Data/raw/master/all_reports.zip
    • https://raw.githubusercontent.com/MosquitoAlert/Data/master/translation_dict.json
    contentSize46MB
variableMeasured
  • @typePropertyValue
    nameversion_UUID
    descriptionUnique identifier randomly generated on the phone to identify each report version. Must be exactly 36 characters long (32 hex digits plus 4 hyphens). Example: D18007F8-FD36-4288-8876-E4314A7B86AA
    qudt:dataTypexsd:string
  • @typePropertyValue
    namecreation_time
    descriptionDate and time on the phone when the first version of the report was created. Already corrected by the 'datetime_fix_offset' value. 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
    namecreation_date
    descriptionDate part of the creation_time string (provided separately for convenience) in YYYY-MM-DD format. Example: 2016-01-03
    qudt:dataTypexsd:string
  • @typePropertyValue
    namecreation_day_since_launch
    descriptionCreation_date expressed as the number of days since June 13, 2014, the day Mosquito Alert was launched (under its former name, Tigatrapp).
    qudt:dataTypexsd:int
  • @typePropertyValue
    namecreation_year
    descriptionYear part of the creation_time string (provided separately for convenience).
    qudt:dataTypexsd:int
  • @typePropertyValue
    namecreation_month
    descriptionMonth part of the creation_time string (provided separately for convenience).
    qudt:dataTypexsd:int
  • @typePropertyValue
    namesite_cat
    descriptionAn integer indicating the type of breeding site recorded by the participant. Options: 0 (storm drain), 1 (fountain), 2 (small basin), 3 (small container), 4 (well), or 5 (other).
    qudt:dataTypexsd:int
    maxValue5
    minValue0
  • @typePropertyValue
    nametype
    descriptionType of report: 'adult', 'site', 'mission', or 'bite'.
    qudt:dataTypexsd:string
  • @typePropertyValue
    namelon
    descriptionLongitude of the report location.
    qudt:dataTypexsd:float
  • @typePropertyValue
    namelat
    descriptionLatitude of the report location.
    qudt:dataTypexsd:float
  • @typePropertyValue
    namemovelab_annotation
    descriptionThis field contains information from the validation process.
    qudt:dataTypexsd:complexType
    value
    • @typePropertyValue
      nameedited_user_notes
      descriptionNotes written by validation experts (or participants edited by validation experts) for display on the public map.
      qudt:dataTypexsd:string
    • @typePropertyValue
      namecrowdcrafting_score_cat
      descriptionTiger mosquito score category assigned to the photo displayed in this report by crowdcrafting volunteers. Scores range from -2 to 2, representing 'Definitely not a tiger mosquito' to 'Definitely a tiger mosquito' respectively.
      qudt:dataTypexsd:string
      maxValue2
      minValue-2
    • @typePropertyValue
      namecrowdcrafting_n_response
      descriptionNumber of crowdcrafting volunteers who have scored the photo displayed in this report.
      qudt:dataTypexsd:int
    • @typePropertyValue
      namesite_certainty_category
      descriptionDegree of belief of experts that at least one photo attached to the report shows an albopictus or aegypti breeding site.
      qudt:dataTypexsd:int
      maxValue2
      minValue-3
    • @typePropertyValue
      nametiger_certainty_category
      descriptionDegree of belief of experts that at least one photo attached to the report shows a tiger mosquito.
      qudt:dataTypexsd:int
      maxValue2
      minValue-3
    • @typePropertyValue
      nameaegypti_certainty_category
      descriptionDegree of belief of experts that at least one photo attached to the report shows an Aedes aegypti adult.
      qudt:dataTypexsd:int
      maxValue2
      minValue-3
    • @typePropertyValue
      namephoto_html
      descriptionAn HTML string that produces a small version of the selected report photo, linked to the original (full-size) version.
      qudt:dataTypexsd:anyURI
    • @typePropertyValue
      namescore
      description
      qudt:dataTypexsd:string
    • @typePropertyValue
      nameclassification
      description
      qudt:dataTypexsd:string
  • @typePropertyValue
    namemovelab_annotation_euro
    descriptionSimilar to 'movelab_annotation' but with preprocessing for machine learning.
    qudt:dataTypexsd:complexType
    value
    • @typePropertyValue
      nameedited_user_notes
      descriptionNotes written by validation experts (or participants edited by validation experts) for display on the public map.
      qudt:dataTypexsd:string
    • @typePropertyValue
      namephoto_html
      descriptionAn HTML string that produces a small version of the selected report photo, linked to the original (full-size) version.
      qudt:dataTypexsd:anyURI
    • @typePropertyValue
      nameclass_name
      descriptionName of the classification label. Available mosquito species labels are: Unclassified (id:1), Other species (id:2), Aedes albopictus (id:3), Aedes aegypti (id:5), Aedes japonicus (id:6), Aedes koreicus (id:7), Complex (id:8), Not sure (id:9), Culex sp. (id:10). Available breeding site labels are: site (id: Null)
      qudt:dataTypexsd:string
    • @typePropertyValue
      nameclass_label
      description
      qudt:dataTypexsd:string
    • @typePropertyValue
      nameclass_id
      description
      qudt:dataTypexsd:int
    • @typePropertyValue
      nameclass_value
      description
      qudt:dataTypexsd:int
  • @typePropertyValue
    nametiger_responses
    descriptionPreprocessed version of 'tiger_responses_text' attribute for machine learning purposes.
    qudt:dataTypexsd:string
  • @typePropertyValue
    nametiger_responses_text
    descriptionAdult mosquito-related user responses stored in JSON format.
    qudt:dataTypexsd:string
  • @typePropertyValue
    namesite_responses
    descriptionPreprocessed version of 'site_responses_text' attribute for machine learning purposes.
    qudt:dataTypexsd:string
  • @typePropertyValue
    namesite_responses_text
    descriptionBreeding site-related user responses stored in JSON format.
    qudt:dataTypexsd:string
  • @typePropertyValue
    nametigaprob_cat
    descriptionTBD
    qudt:dataTypexsd:int
  • @typePropertyValue
    namevisible
    description
    qudt:dataTypexsd:boolean
  • @typePropertyValue
    namelatest_version
    description
    qudt:dataTypexsd:boolean
  • @typePropertyValue
    namen_photos
    description
    qudt:dataTypexsd:int
  • @typePropertyValue
    namefinal_expert_status_text
    description
    qudt:dataTypexsd:int
  • @typePropertyValue
    nameresponses
    descriptionBites-related user responses stored in JSON format with the following keys: 'id' identifier; 'translated_question' question as it was in the app, translated to the same language the app was when uploading the report (if the app is in a language which have not translation yet, it defaults to english); 'translated_answer' user's answer to the question; 'question_id' question identifier; 'question' text format question in default language; 'answer_id' answer identifier; 'answer' text format answer in default language; 'answer_value' integer value relative to the answer; 'report' identifier of the report.
    qudt:dataTypexsd:string
  • @typePropertyValue
    namecountry
    descriptionISO3166-1 alpha3 country codes for the European Union. Absence indicates the report does not fall within an EU country.
    qudt:dataTypexsd:string
  • @typePropertyValue
    nameupdated_at
    descriptionDate and time when the report was last modified. 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
    namedatetime_fix_offset
    descriptionAn integer representing the offset (in seconds) applied to the original datetime values for fixing. If None, it indicates that no information about the original time zone could be inferred or the timezone was already provided when posting the report. To retrieve the original buggy values, use: original_buggy_value = current_value - datetime_fix_offset.
    qudt:dataTypexsd:int
  • @typePropertyValue
    namecached_visible
    descriptionTBD
    qudt:dataTypexsd:float
  • @typePropertyValue
    namepoint
    descriptionCoordinate point lat/lon values with the relative Spatial Reference System Identifier (SRID) in Well-Known Binary (WKB) format.
    qudt:dataTypexsd:string
  • @typePropertyValue
    namenuts_3
    descriptionNUTS statistical regions for the European Union on level 3.
    qudt:dataTypexsd:string
  • @typePropertyValue
    namenuts_2
    descriptionNUTS statistical regions for the European Union on level 2.
    qudt:dataTypexsd:string
  • @typePropertyValue
    namesession
    description
    qudt:dataTypexsd:float
measurementTechnique
  • Sampling. Anonymous citizen scientists send reports of possible observations of mosquitoes, their breeding sites and bites using the open source and free smartphone app Mosquito Alert. To send an observation, participants need to answer a small questionnaire (taxonomic questions in the case of mosquitoes or some descriptors in the case of breeding sites), indicate the location (current participant location or selecting it on a map), add a picture (optional) and notes or comments (optional). The app and project website offers information to help identify the target species and take good pictures that allow a proper post validation from entomologists (see more information onQuality Control section). Participants can edit or remove the observation at any time (only if the participant still maintains the Mosquito Alert app in their phone). The last version of each report is considered the prevailing information. There is no pre-set sampling frequency: participants can send as many data as they like. The project runs "face-to-face data collection events" mainly in schools, meaning that in some places and for a given time period, data sampling might be more intense. This is also true when and where there has been a particular dissemination event.
  • Quality control. Each report containing at least one picture evaluated by three independent entomologist and, if needed, reviewed by a fourth expert(senior entomologist). The dataset only includes reports from citizen staged by them as "adult mosquito", that contain at least one picture and that it has been evaluated by entomological experts.
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": "97de27fc", "metadata": { "papermill": { "duration": 0.007522, "end_time": "2024-07-01T13:29:15.293940", "exception": false, "start_time": "2024-07-01T13:29:15.286418", "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": 1.500967, "end_time": "2024-07-01T13:29:15.621817", "environment_variables": {}, "exception": null, "input_path": "build_info.ipynb", "output_path": "./meta_ipynb/reports.ipynb", "parameters": { "path": "./meta/mosquito_alert/reports" }, "start_time": "2024-07-01T13:29:14.120850", "version": "2.3.4" } }, "nbformat": 4, "nbformat_minor": 5 }