OncoKB 爬虫获取位点用药信息_oncokb数据库-CSDN博客

本文链接：https://blog.csdn.net/weixin_46918050/article/details/145595295

OncoKB 官网：OncoKB™ - MSK's Precision Oncology Knowledge Base

一、思路：

1、首先我们要获取genes的列表

2、然后以genes列表的每个gene获取对应的突变信息和药物信息

例：以EGFR为例

gene详情

突变信息

具体突变的用药信息

FDA认证数据

这几大类就是我们要获取的重要信息

下来我们开始具体的操作：

第一步获取oncoKB现有gene列表

进入oncoKB主页，点击genes（现在更新有905个gene）

点击

进入到gene列表页面（第一种直接下载列表cancerGeneList.tsv ）

第二种（打开f12开发者工具获取api接口数据）

详细代码获取api接口

 String url = "https://www.oncokb.org/api/v1/utils/cancerGeneList";
       
 //gene列表list
 int count = 0;
 List<String> geneList = new ArrayList<>();
 JsonNode geneNode = getHttpJsonNode(url);
 for (JsonNode node : geneNode) {
       String hugoSymbol = node.get("hugoSymbol").asText();
       geneList.add(hugoSymbol);
  }

这是一个通用的HTTP调用工具代码后面好多地方都会用到

public static JsonNode getHttpJsonNode(String url) throws IOException {

        try (CloseableHttpClient httpClient = HttpClients.createDefault()) {
            HttpGet httpGet = new HttpGet(url);
            httpGet.setHeader("Content-Type", "application/json");
            httpGet.setHeader("Authorization", "Basic " + 
            httpGet.setHeader("Accept", "text/html,application/xhtml+xml,application/xml;q=0.9,image/avif,image/webp,image/apng,*/*;q=0.8,application/signed-exchange;v=b3;q=0.7");
            httpGet.setHeader("Accept-Encoding", "gzip, deflate, br");
            httpGet.setHeader("Accept-Language", "zh-CN,zh;q=0.9");
            httpGet.setHeader("User-Agent", "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/116.0.0.0 Safari/537.36");

            HttpResponse response = httpClient.execute(httpGet);
            HttpEntity entity = response.getEntity();
            String responseBody = EntityUtils.toString(entity);

            // 创建 ObjectMapper 对象
            ObjectMapper objectMapper = new ObjectMapper();
            // 使用 ObjectMapper 将 JSON 字符串转换为 JsonNode 对象
            JsonNode jsonNode = objectMapper.readTree(responseBody);
            return jsonNode;

        }
    }

获取gene详情数据

详细代码（通用的http请求代码上面已经说过了）

String url1 = "https://www.oncokb.org/api/private/search/variants/biological?hugoSymbol=#{gene}";
        //gene列表list
        List<String> geneList = new ArrayList<>();
       
        for (String gene : geneList) {
            String url11 = url1.replace("#{gene}",gene);
            JsonNode annotNode = getHttpJsonNode(url11);
            for (JsonNode jsonNode : annotNode) {
                JsonNode variant = jsonNode.get("variant");
                String alteration = variant.get("alteration").asText();
                String oncogenic = jsonNode.get("oncogenic").asText();
                String mutationEffect = jsonNode.get("mutationEffect").asText();
                String mutationEffectDescription =    jsonNode.get("mutationEffectDescription").asText();
             }
         }

获取具体药物数据

详细代码

String url1 = "https://www.oncokb.org/api/private/search/variants/clinical?hugoSymbol=#{gene}";
//gene列表list
List<String> geneList = new ArrayList<>();
for (String gene : geneList) {
            String url11 = url1.replace("#{gene}",gene);
            JsonNode therapeuticNode = getHttpJsonNode(url11);
            for (JsonNode jsonNode : therapeuticNode) {
                String level = jsonNode.get("level").asText();
                JsonNode variant = jsonNode.get("variant");
                String alteration = variant.get("name").asText();
                String levelAssociaCancerType = jsonNode.get("cancerTypes").get(0).get("subtype").asText();
                JsonNode drugsnode = jsonNode.get("drug");
                String drugs = "";
                for (int i = 0; i < drugsnode.size(); i++) {
                    String drug = drugsnode.get(i).asText();
                    drugs += drug;
                    if (i != drugsnode.size() - 1){
                        drugs += " + ";
                    }
                }
                String drugDescription = jsonNode.get("drugDescription").asText();
          }
}

FDA也包含在这个api中由fdaLevel来区分