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Large-Scale Event Extraction from Literature with Multi-Level Gene…

- - - - 消除了gene symbol拼写多样性问题，以及前后缀问题,见文章中ESR的例子
      - does not resolve synonymy or the species of gene mentions, so that it does not alone allow for a reliable mapping to database identifiers.
    - - The reasoning behind the family-based assignment is that homologous genes evolved from a common ancestor, often still exhibit similar functional behavior, and are consequently assigned to similar names which is hard to distinguish in biological literature.
      - 老版本EVEX仅仅基于Canonical form来assign gene family, disambiguation见文章，但是效果不好，因为很有可能率属于不同gene family的gene在文章中的gene symbol（也就是canonical form）相同
    - - 使用GenNorm normalization algorithm, for assign organism-specific(organism指的貌似是这个基因或是protein是哪个organ的，比如MEC1这个基因，也可以说是蛋白质编码，它的organ就是Saccharomyces cerevisiae酒酿酵母的) Entrez Gene identifiers（Entrez也是一个结构化的生物数据库,比如刚才MEC1在这个数据库里的链接就是https://www.ncbi.nlm.nih.gov/gene/852433/）
      - GenNorm is a method for cross species gene normalization
    - - combination 3——for unique family id
        
        if GenNorm algorithm produce a unique gene identifier
        
        query EVEX database to determine whether the gene ID, assigned by GenNorm is linked to a known gene family and assign that family accordingly.
        
        if GenNorm fails to produce a unique gene identifier(multiple gene identifiers)
        
        apply adapted version of the original symbol-based family assignment as fall back: taking into account both the canonical form of the gene mention and organism assigned by GenNorm, assign a family that contains at least one (间接证明multiple identifiers)gene of the specified organism. When there are multiple candidate families, the family is picked that contains the most genes with this specific canonical form as synonym.
        
        if there is no candidate family matching the organism assignment(and there is no id assigned by GenNorm)
        
        original symbol-based algorithm is applied
      - combination 2——for unique species and Gene ID
        
        due to the inter-species ambiguity of a specific gene symbol, GenNorm may assign multiple gene ids to a mention
        
        the fallback procedure of the family assignment(combination 3的第二种情况)，will assign a family(这个family考虑了canonical的信息). When this family contains a gene of the organism determined by GenNorm, 我们就可以从multiple IDs中筛选出最终的ID。
      - combination 1——for unique gene and species ID
        
        a significant proportion of gene symbols are unique within one species and can thus be assigned based solely on the canonical symbol and species.
- - - - 使用的entity recognition工具BANNER scope太广，给Gene normalization造成了难度（normalization的scope没有完全涵盖BANNER的范围）
      - 主要原因是：本文使用的这个event pipeline处理不了table以及figure，which里面有很多在单独使用GenNorm时可以被标注的Gene，所以这就造成了大量false negative的出现，所以本文未来工作就是看看能不能把不能处理table以及figure这个问题解决。
      - 接下来分析了combination方法对于gene normalization的效果。注意本文的衡量的貌似有两种combination结构，比如说表4中Canonical是指updated canonicalization algorithm using the taxonomic assignments of GenNorm(Combination 1 figure 2)，然而Canonical +GenNorm则用到了fallback mechanism(有什么priority 和fallback，总之我也没太懂)，然后gene family有三种不同定义HomoloGene，Ensembl，Ensembl GenNorm，这样就有三种Combination 2，本文分别做了实验。
        
        得到的结论就是Canonical很好，然后family具体的方法有各自的特点 blablabla