建华，我认为我们需要试着理清通过KEGG可以/不可以得到什么。我已经开始编写包，但我希望您做很多基本的实现和文档。大多数类型等都可以从KEGG的网页，我们确实需要一个可行的版本在8月的第一周结束，因为我想在书中有一些。据我所知，我们将需要一些他们正在使用的三个字母的物种缩写的清单，这样人们就可以请求特定物种的路径数据。我不确定这对KEGG的数据有什么影响，因为我认为我们现在的数据是不正确的。环境:KEGGPATHID2EXTID和KEGGEXTID2PATHID不可能是正确的，我猜我们需要把它们留给某种特定于生物体的数据库或KEGGSOAP包。例如:大多数get_xxx函数将返回带有这些槽位的对象。我认为我们不需要S4课程，但我们应该记录下将会发生什么。返回类型:genes_id1查询的genes_id(字符串)genes_id2目标的genes_id(字符串)sw_score genes_id1和genes_id2之间的Smith-Waterman分数(int) bit_score genes_id1和genes_id2之间的比特分数(float) identity genes_id1和genes_id2之间的身份(float) overlap重叠长度(int) start_position1 genes_id1中对齐的起始位置(int) end_position1 genes_id1中对齐的结束位置(int) start_position2开始位置 alignment in genes_id2 (int) end_position2 end position of the alignment in genes_id2 (int) best_flag_1to2 best-best flag from genes_id1 to genes_id2 (boolean) best_flag_2to1 best-best flag from genes_id2 to genes_id1 (boolean) definition1 definition string of the genes_id1 (string) definition2 definition string of the genes_id2 (string) length1 amino acid length of the genes_id1 (int) length2 amino acid length of the genes_id2 (int) Also, I found a lot of examples at: http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioruby/lib/bio/io/keggapi.rb?cvsroot=bioruby&rev=1.5 (just search on something like get_motifs_by_gene at Google and this comes up. It seems to have some sensible values. Here are some examples that I have got to go, together with my simple package example. Which is on rna in ~rgentlem/Rpacks/KEGGSOAP and the SSOAP that I have done some surgery on is there as well. g1 = get_best_neighbors_by_gene("eco:b0002",1, 5) sapply(g1, function(x) x$genes_id2) g2 = get_genes_by_pathway("path:hsa00020") g3 = get_genes_by_pathway("path:eco00020") g4 = get_genes_by_pathway("path:ddi00020") dbs = list_databases() xx=get_motifs_by_gene("eco:b0002", "pfam")