Data_Melioidosis_1910_2014

The occurrence data set was comprised of geo-located records of human cases, animal cases and presence of B. pseudomallei in the environment derived from (i) peer reviewed literature and (ii) case reports (see Extended Data Figure 1, Panel a). For peer reviewed literature, we searched Pubmed, Genbank database (http://www.ncbi.nlm.nih.gov/genbank), MLST database (http://bpseudomallei.mlst.net) and Eurosurveillance database (http://eurosurveillance.org) for studies describing human cases, animal cases or presence of B. pseudomallei in the environment between Jan 1,1920 and Dec 31, 2014 using the MeSH terms “melioidosis” or “pseudomallei”. No language restrictions were placed on these searches, however, only those citations with a full title and abstract were retrieved. We searched bibliographies from selected studies for secondary references. For case reports, we searched ProMED (http://www.promedmail.org), and Ministry of Health websites for each country. We also searched GoogleNews archives (http://news.google.co.utk/archive search) using the same search terms and country name for news and reports of melioidosis at a country level.
An occurrence was defined as the reporting of a case of melioidosis infection or identification of B. pseudomallei at an environmental sampling point. All occurrence data underwent manual review and automated quality control procedures to ensure information fidelity and precise geo-positioning (e.g. duplicate records were excluded). All available location information was extracted from each peer-reviewed article and case reports. If the literature reported cases at more than one location, we disaggregated the cases to separate occurrence records. Imported cases were included if clear information about the location where the infection originated was available, and these source locations were entered into the database. The site name was used together with all contextual information provided about the site position to determine its latitudinal and longitudinal coordinates using Google Maps (https://www.maps.google.co.uk/). If the year of occurrence was not reported, the year of the publication or report was used. After processing, a total of 22,338 geo-located occurrences spanning a period from 1910 to 2014 were included.
Each of the 22,338 rows represents a single occurrence record of either human melioidosis case, animal melioidosis case or presence of B. pseudomallei in the environment. The fields contained in the database are as follows:
1. OCCURRENCE_ID: Unique identifier for each occurrence in the database after temporal and locational standardisation
2. OCCURRENCE_TYPE: Whether the record represents human melioidosis case, animal melioidosis case or presence of B. pseudomallei in the environment
3. OCCURRENCE_EXPORT: Whether the record represents the export event
4. SOURCE: The details of the source
5. YEAR: The year of occurrence
6. REGION: The region where the occurrence lies – values are East Asia & Pacific, Europe & Central Asia, Latin America & Caribbean, Middle East & North Africa, South Asia and Sub-Saharan Africa.
7. COUNTRY: The name of the country where the occurrence lies
8. LOCATION: The name of the location where the occurrence lies
9. LAT: The latitudinal coordinate of the point or polygon centroid (WGS 1984 Datum)
10. LONG: The longitudinal coordinate of the point or polygon centroid (WGS 1984 Datum)

本发生数据集由人类病例、动物病例以及环境中的B. pseudomallei存在记录的地理位置信息组成，这些信息来源于(i)同行评审文献和(ii)病例报告（参见扩展数据图1，面板a）。对于同行评审文献，我们检索了PubMed、Genbank数据库（http://www.ncbi.nlm.nih.gov/genbank）、MLST数据库（http://bpseudomallei.mlst.net）和Eurosurveillance数据库（http://eurosurveillance.org），以寻找描述人类病例、动物病例或环境中B. pseudomallei存在的相关研究，研究时间范围为1920年1月1日至2014年12月31日，使用MeSH术语“melioidosis”或“pseudomallei”。在搜索过程中未对语言进行限制，但仅检索了具有完整标题和摘要的参考文献。对于次级参考文献，我们检索了选定研究的参考文献目录。对于病例报告，我们检索了ProMED（http://www.promedmail.org）以及各国卫生部的网站。我们还使用相同的搜索术语和各国名称，通过GoogleNews存档（http://news.google.co.utk/archive search）检索了关于各国的melioidosis新闻报道和报告。一次发生事件被定义为melioidosis感染病例的报告或环境采样点的B. pseudomallei鉴定。所有发生数据均经过人工审查和自动化质量控制程序，以确保信息真实性及精确的地理位置定位（例如，排除重复记录）。从每一篇同行评审文章和病例报告中提取了所有可用的地理位置信息。如果文献报告了多个地点的病例，我们将病例分解为单独的发生记录。如果关于感染起源地的位置信息明确，则将输入病例包括在内，并将这些来源地输入数据库。使用Google Maps（https://www.maps.google.co.uk/）结合有关地点位置的所有上下文信息来确定其经纬度坐标。如果未报告发生年份，则使用出版或报告的年份。处理后，共纳入了22,338个地理位置信息，时间跨度为1910年至2014年。22,338行中的每一行代表人类melioidosis病例、动物melioidosis病例或环境中B. pseudomallei存在的一次单独发生记录。数据库中包含的字段如下：
1. OCCURRENCE_ID：数据库中每个发生事件的唯一标识符，经过时间和地理位置标准化后
2. OCCURRENCE_TYPE：记录是否代表人类melioidosis病例、动物melioidosis病例或环境中B. pseudomallei的存在
3. OCCURRENCE_EXPORT：记录是否代表出口事件
4. SOURCE：来源的详细信息
5. YEAR：发生年份
6. REGION：发生事件的地区 – 值为东亚及太平洋、欧洲及中亚、拉丁美洲及加勒比海、中东及北非、南亚和撒哈拉以南非洲
7. COUNTRY：发生事件的国家的名称
8. LOCATION：发生事件的地点名称
9. LAT：点或多边形质心的纬度坐标（WGS 1984坐标系
10. LONG：点或多边形质心的经度坐标（WGS 1984坐标系）