R科研作图学习小组

http://group.keyangou.com/RGraph
组长: 管理员:
  • 访问次数:28572
  • 小组等级:9
  • 话题:593
  • 回答:39
  • 签到:439
  • 小组排名:
  • R2-01第二阶段-1—Pubmed接口获得初步数据

    木萱小主 发布于:2018.01.15

    任务1:

    install.packages("httr")
    install.packages("xml2")
    library(httr)
    library(xml2)
    baseUrl="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"

    searchArticleParam=list(retstart=0,retmax=20,usehistory='Y',querykey='',webenv='',term='(cell[TA]) AND 2017[DP]',total_num=0,total_page=1,  page_size=20, current_page=1)
    r<-POST(baseUrl,body=list(db='pubmed',term=searchArticleParam$term,retmode='json',retstart=searchArticleParam$retstart,retmax=searchArticleParam$retmax,usehistory=searchArticleParam$usehistory,
    rettype='uilist'))
    stop_for_status(r)
    data=content(r, "parsed","application/json")
    data
    esearchresult=data$esearchresult
    count=esearchresult$count
    print(count)

    count =563

     任务2

    baseUrl2="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
    pubmedid="29275861,29275860";
    searchArticleParam$total_num=esearchresult$count
    searchArticleParam$querykey=esearchresult$querykey
    searchArticleParam$webenv=esearchresult$webenv
    r2<-POST(baseUrl2,body=list(db='pubmed',id=pubmedid,retmode='xml',querykey=searchArticleParam$querykey,webenv=searchArticleParam$webenv))
    data2=content(r2,"parsed")
    article=xml_children(data2)
    count=length(article)
    cnt=1
    while(cnt<=count){title=xml_find_first(article[cnt],".//ArticleTitle")
    abstract=xml_find_first(article[cnt],".//AbstractText")
      print(xml_text(title))
      print(xml_text(abstract))
      cnt = cnt + 1
    }

     "Natural Killer Cells Control Tumor Growth by Sensing a Growth Factor."
    [1] "Many tumors produce platelet-derived growth factor (PDGF)-DD, which promotes cellular proliferation, epithelial-mesenchymal transition, stromal reaction, and angiogenesis through autocrine and paracrine PDGFRβ signaling. By screening a secretome library, we found that the human immunoreceptor NKp44, encoded by NCR2 and expressed on natural killer (NK) cells and innate lymphoid cells, recognizes PDGF-DD. PDGF-DD engagement of NKp44 triggered NK cell secretion of interferon gamma (IFN)-γ and tumor necrosis factor alpha (TNF-α) that induced tumor cell growth arrest. A distinctive transcriptional signature of PDGF-DD-induced cytokines and the downregulation of tumor cell-cycle genes correlated with NCR2 expression and greater survival in glioblastoma. NKp44 expression in mouse NK cells controlled the dissemination of tumors expressing PDGF-DD more effectively than control mice, an effect enhanced by blockade of the inhibitory receptor CD96 or CpG-oligonucleotide treatment. Thus, while cancer cell production of PDGF-DD supports tumor growth and stromal reaction, it concomitantly activates innate immune responses to tumor expansion."
    [1] "Antigen Identification for Orphan T Cell Receptors Expressed on Tumor-Infiltrating Lymphocytes."
    [1] "The immune system can mount T cell responses against tumors; however, the antigen specificities of tumor-infiltrating lymphocytes (TILs) are not well understood. We used yeast-display libraries of peptide-human leukocyte antigen (pHLA) to screen for antigens of \"orphan\" T cell receptors (TCRs) expressed on TILs from human colorectal adenocarcinoma. Four TIL-derived TCRs exhibited strong selection for peptides presented in a highly diverse pHLA-A∗02:01 library. Three of the TIL TCRs were specific for non-mutated self-antigens, two of which were present in separate patient tumors, and shared specificity for a non-mutated self-antigen derived from U2AF2. These results show that the exposed recognition surface of MHC-bound peptides accessible to the TCR contains sufficient structural information to enable the reconstruction of sequences of peptide targets for pathogenic TCRs of unknown specificity. This finding underscores the surprising specificity of TCRs for their cognate antigens and enables the facile indentification of tumor antigens through unbiased screening."


     

     

     
    2条评论 321浏览 邀请回答

    真·科研狗 回答于:2018年01月15日 20:22:351楼

     北京大学 医学部基础医学院 细胞生物学 博士 

    你得到了这个数据,但是需要解析出来,在程序里面得到count=xxx,print(count),用xml2去解析即可

    木萱小主 回答于:2018年01月18日 09:47:322楼

    北京 北京协和医学院 微生物与生化药学博士 
    #真·科研狗# 在2018-01-15 20:22:35说到:

    你得到了这个数据,但是需要解析出来,在程序里面得到count=xxx,print(count),用xml2去解析即可

    恩恩 多谢


    小组告示

    科研狗 2012-2016 京ICP备16006621 科研好助手,专业的科研社交共享平台