nuget
biological object query helper module
SMRUCC.genomics.Core 10.5.9762.7562.
01 Namespaces
SMRUCC.genomics
| Type | Summary | Members |
|---|---|---|
| BioAssemblyExtensions | Extension methods for some common operations | 9 |
| LICENSE | ᶘ ᵒᴥᵒᶅ？？？？ | 6 |
SMRUCC.genomics.Assembly.Bac_sRNA.org
| Type | Summary | Members |
|---|---|---|
| Interaction | Interaction.sRNAid --> Interaction.TargetName | 7 |
| Sequence | 5 |
SMRUCC.genomics.Assembly.DOMINE.Tables
| Type | Summary | Members |
|---|---|---|
| Go | 4 | |
| Interaction | 22 | |
| Pfam | 5 | |
| PGMap | 3 |
SMRUCC.genomics.Assembly.DOOR
| Type | Summary | Members |
|---|---|---|
| DOOR | DOOR: Database of prOkaryotic OpeRons. | 9 |
| DOOR_API | We present a database DOOR (Database for prOkaryotic OpeRons) containing computationally predicted operons of all the sequenced prokaryotic genomes. | 6 |
| DOOR_IO | Parser and writer | 3 |
| Operon | 操纵子中的基因在构造函数之中已经进行过按照转录方向排序操作了的 | 14 |
| OperonGene | Door操纵子之中的一个基因对象的数据 | 3 |
| OperonView | {OperonID, GeneId()}() | 3 |
SMRUCC.genomics.Assembly.DOOR.CsvModel
| Type | Summary | Members |
|---|---|---|
| Operon | 5 |
SMRUCC.genomics.Assembly.ELIXIR.EBI.ChEBI
| Type | Summary | Members |
|---|---|---|
| AccessionTypes | Chebi accession types, table key name in RegistryNumbers | 74 |
| DATA | Chebi ChEBIEntity model extensions | 8 |
| EntitySearch | 4 | |
| EntitySummary | 物质注释信息摘要表格 | 15 |
| Extensions | 5 | |
| NameOf | 使用这个模块进行chebi的编号的匹配， (由于有同分异构体之类的存在，所以即使化学式或者分子质量相同，也会匹配出几种不同的化合物， 所以NameOf.MatchByFormula())以及NameOf.MatchByMass()) 这两个方法应该是优先级别最低的) | 15 |
SMRUCC.genomics.Assembly.ELIXIR.EBI.ChEBI.Database.IO.StreamProviders.Tsv
| Type | Summary | Members |
|---|---|---|
| Compound | 1 | |
| TsvExtensions | Extension for ChEBI tsv tables entity. | 3 |
| TSVTables | 可以使用这个对象从ChEBI的ftp文件夹下载结果之中加载相应的表数据 | 8 |
SMRUCC.genomics.Assembly.ELIXIR.EBI.ChEBI.Database.IO.StreamProviders.Tsv.Tables
| Type | Summary | Members |
|---|---|---|
| Accession | Database xref dblinks.(ChEBI的ftp服务器之上的database_accession.tsv文件数据的解析器) | 3 |
| ChemicalData | chemical_data.tsv | 5 |
| Entity | 5 | |
| InChI | chebiId_inchi.tsv | 2 |
SMRUCC.genomics.Assembly.ELIXIR.EBI.ChEBI.Database.IO.StreamProviders.Tsv.TSVTables
| Type | Summary | Members |
|---|---|---|
| FileNames | 15 |
SMRUCC.genomics.Assembly.ELIXIR.EBI.ChEBI.WebServices
| Type | Summary | Members |
|---|---|---|
| WebServices | The main aim of ChEBI Web Services is to provide programmatic access to the ChEBI database in order to aid our users in integrating ChEBI into their applications. | 4 |
SMRUCC.genomics.Assembly.ELIXIR.EBI.ChEBI.XML
| Type | Summary | Members |
|---|---|---|
| ChEBIEntity | The complete entity including synonyms, database links and chemical structures. | 2 |
| Extensions | 1 | |
| Formulae | 分子式 | 3 |
SMRUCC.genomics.Assembly.Expasy.AnnotationsTool
| Type | Summary | Members |
|---|---|---|
| API | 4 | |
| EnzymeClass | 这个是最终的酶分类结果的呈现形式 | 3 |
| T_EnzymeClass_BLAST_OUT | The raw annotation data which was export from the blast output text.(蛋白酶的酶编号分类（这个数据结构是用来表示blast比对结果的）) | 1 |
SMRUCC.genomics.Assembly.Expasy.AnnotationsTool.API
| Type | Summary | Members |
|---|---|---|
| _____ENZYME_CLASS_HANDLER_ | Handler for process the duplicated enzyme classification data. | 0 |
SMRUCC.genomics.Assembly.Expasy.Database
| Type | Summary | Members |
|---|---|---|
| Enzyme | 使用Uniprot编号为主的酶分类数据记录 | 8 |
| NomenclatureDB | ENZYME nomenclature database.(Expasy数据库之中的enzyme.dat注释文件) | 3 |
SMRUCC.genomics.Assembly.iGEM
| Type | Summary | Members |
|---|---|---|
| PartSeq | 1 |
SMRUCC.genomics.Assembly.KEGG
| Type | Summary | Members |
|---|---|---|
| Extensions | 12 | |
| ReactionClassifier | the reaction class data helper, make index of the ReactionClass data | 5 |
| ReactionRepository | KEGG的参考代谢反应模型库，封装了对Reaction的对象查询操作 | 10 |
SMRUCC.genomics.Assembly.KEGG.Archives
| Type | Summary | Members |
|---|---|---|
| SequenceDump | 1 |
SMRUCC.genomics.Assembly.KEGG.Archives.Tabular
SMRUCC.genomics.Assembly.KEGG.Archives.Xml
| Type | Summary | Members |
|---|---|---|
| CompilerAPI | 1 | |
| MapAPI | 3 | |
| XmlModel | The compile data of the target bacteria species genome database in the KEGG.(KEGG数据库之中的关于目标研究的微生物菌株的KEGG数据库之中的所有的信息的编译的集合) | 4 |
SMRUCC.genomics.Assembly.KEGG.Archives.Xml.Nodes
| Type | Summary | Members |
|---|---|---|
| EC_Mapping | 3 | |
| PwyBriteFunc | 2 |
SMRUCC.genomics.Assembly.KEGG.DBGET
| Type | Summary | Members |
|---|---|---|
| KEGGObjects | KEGG数据库之中的对象的类型的列表 | 20 |
| KOrthology | KEGG Orthology | 9 |
SMRUCC.genomics.Assembly.KEGG.DBGET.bGetObject
| Type | Summary | Members |
|---|---|---|
| bGetObject | dbget-bin/www_bget | 4 |
| Compound | A data model for the KEGG compound. | 6 |
| Disease | 1 | |
| Glycan | 1 | |
| Hsa_gene | The data model of the genes in the human genome.(人类基因组之中的基因模型) | 3 |
| Module | KEGG MODULE is a collection of manually defined functional units, called KEGG modules and identified by the M numbers, used for annotation and biological interpretation of sequen… | 1 |
| OrthologyTerms | 2 | |
| Pathway | The kegg pathway annotation data. | 6 |
| PathwayMap | Pathway.LoadFromResource(). | 7 |
| Reaction | KEGG reaction annotation data. | 10 |
| ReactionClass | represents a collection of the kegg Reaction data model which are have similar compound structure transformation result. | 2 |
| ReactionCompoundTransform | 反应左端代谢物在经过了代谢反应之后结果上的转换变化的结果（反应的右端） | 3 |
| Reference | 参考文献 | 8 |
SMRUCC.genomics.Assembly.KEGG.DBGET.bGetObject.Organism
| Type | Summary | Members |
|---|---|---|
| EntryAPI | 10 | |
| KEGGOrganism | KEGG Organisms: Complete Genomes (http://www.genome.jp/kegg/catalog/org_list.html) | 1 |
| Organism | 4 | |
| OrganismInfo | http://www.kegg.jp/kegg-bin/show_organism?org={code} | 7 |
| Prokaryote | 原核生物 | 2 |
| ShowOrganism | http web handler for the kegg organism info page | 0 |
SMRUCC.genomics.Assembly.KEGG.DBGET.bGetObject.SSDB
| Type | Summary | Members |
|---|---|---|
| Enzyme | 9 | |
| Ortholog | .csv > http://www.kegg.jp/ssdb-bin/ssdb_best?org_gene=sp:locus_tag | 15 |
| OrthologREST | 蛋白质直系同源比对blastp结果, *.xml | 9 |
| Orthology | KEGG KO分类 | 1 |
SMRUCC.genomics.Assembly.KEGG.DBGET.BriteHEntry
| Type | Summary | Members |
|---|---|---|
| BriteHText | BRITE Functional Hierarchies | 11 |
| BriteHTextParser | 2 | |
| BriteTerm | A general brite term | 6 |
| CompoundBrite | Compounds with Biological Roles.(在这里面包含有KEGG compounds的下载API) | 32 |
| EnzymaticReaction | Extract data from the htext entry model | 5 |
| EnzymeEntry | 在这里的entry是KO编号，而非Reaction编号 | 6 |
| htext | KEGG BRITE is a collection of manually created hierarchical text (htext) files capturing functional hierarchies of various biological objects, especially those represented as K… | 7 |
| KOCatalog | 1 | |
| ModsBrite | 加载代谢途径或者KEGG Modules的Brite文档的模块 | 3 |
| Module | KEGG里面的模块的入口点的定义数据 | 7 |
| ModuleClassAPI | 4 | |
| Organism | br08601 > http://www.kegg.jp/kegg-bin/download_htext?htext=br08601.keg&format=htext&filedir= | 2 |
| Pathway | The brief entry information for the pathway objects in the KEGG database. | 7 |
| PathwayProfiles | 2 | |
| ReactionClass | 5 |
SMRUCC.genomics.Assembly.KEGG.DBGET.LinkDB
| Type | Summary | Members |
|---|---|---|
| Relationships | 9 |
SMRUCC.genomics.Assembly.KEGG.DBGET.ReferenceMap
| Type | Summary | Members |
|---|---|---|
| ReferenceMapData | KEGG数据库之中的参考途径 | 1 |
| ReferenceReaction | 1 |
SMRUCC.genomics.Assembly.KEGG.Medical
| Type | Summary | Members |
|---|---|---|
| ClassInheritance | 4 | |
| Disease | 1 | |
| Drug | 药物分子的注释信息 | 0 |
| DrugParser | 解析KEGG ftp服务器上面的药物数据模型 | 3 |
| Extensions | 2 |
SMRUCC.genomics.Assembly.KEGG.WebServices
| Type | Summary | Members |
|---|---|---|
| FetchSequence | 1 | |
| ListEntry | Search entry | 7 |
| LocalRender | KEGG pathway map local rendering engine | 10 |
| MapHighlights | mix rendering | 2 |
| MapIndex | a subclass of Map | 1 |
| MapRepository | The repository xml data of kegg Map | 5 |
| PathwayMapping | 需要程序处于联网状态 | 11 |
| QueryEntry | 5 | |
| QuerySource | Meta data for query KEGG database | 6 |
| URLEncoder | The kegg pathway map url encoder pattern: http://www.genome.jp/kegg-bin/show_pathway?{pathway_ID}/{geneID}%09{color}/{geneID}%09{color}/{geneID}%09{color} | 6 |
| WebRequest | KEGG web query request handler.(KEGG数据库web查询处理模块) KEGG是一个代谢图，收录基因和基因组的数据库，数据库可以分为 3 大部分，基因数据库，化学分子物质数据库，以及基于基因和化学分子物质相互关系而建立起来的代谢路径数据库， 在KEGG数据库中，有一个“专有名词”KO（KEGG Orthology），它是… | 17 |
SMRUCC.genomics.Assembly.KEGG.WebServices.InternalWebFormParsers
| Type | Summary | Members |
|---|---|---|
| WebForm | parser for the kegg form data text, example like request text content from the rest: https://rest.kegg.jp/get/hsa00592 (KEGG 网页表格的数据解析方法，在Value之中可能会有重复的Key数据出现) | 8 |
SMRUCC.genomics.Assembly.KEGG.WebServices.KGML
| Type | Summary | Members |
|---|---|---|
| entry | Network nodes | 6 |
| GeneMetaboliteNetwork | A network of gene -> compound that is extracted from the KGML metabolic reaction data. | 9 |
| GeneNetworkExport | A network of gene1 -> compound -> gene2 | 10 |
| link | Network edges | 2 |
| pathway | The kegg pathway map layout data in KGML file format. | 6 |
| reaction | <reaction>元素表示通路中的一种生化反应，用于连接代谢物节点，形成代谢网络中的化学转化关系。在代谢通路中，<reaction>元素主要涉及底物（substrates） 和产物（products）两类代谢物节点。它描述了一个化学反应如何将一组底物转化为另一组产物，以及该反应是否可逆等信息。<reaction>元素在KGML中通常用于 表示化学网络（… | 4 |
| relation | <relation>元素表示通路中两个节点之间的关联关系，主要用于描述蛋白质（或基因产物）之间的相互作用，以及蛋白质与代谢物之间的调控关系。与<reaction>描述化学转化不同， <relation>更侧重于调控和相互作用，例如一个蛋白质激活或抑制另一个蛋白质，或一个蛋白质结合一个代谢物等。<relation>元素在KGML中通常用于表示蛋白质网络（pr… | 3 |
SMRUCC.genomics.Assembly.KEGG.WebServices.WebRequest
| Type | Summary | Members |
|---|---|---|
| GetFastaSequenceMethod | The unify interface for gets the data from KEGG database.(从KEGG数据库获取序列数据以及从本底的数据库之中获取序列数据的统一接口) | 1 |
SMRUCC.genomics.Assembly.KEGG.WebServices.XML
SMRUCC.genomics.Assembly.MetaCyc
| Type | Summary | Members |
|---|---|---|
| Extensions | 1 |
SMRUCC.genomics.Assembly.MetaCyc.File
| Type | Summary | Members |
|---|---|---|
| AttributeValue | Attribute-Value: Each attribute-value file contains data for one class of objects, such as genes or proteins. | 2 |
| Classes | The class types that appears in the MetaCyc database. | 5 |
| FileReader | Database file reader of the metacyc database. | 3 |
| ObjectModel | 每一个数据文件里面的每一个对象的模型 | 0 |
| Property | The summary database property text content in the attribute-value data file head line. | 9 |
| TabularFile | Each tabular file contains data for one class of objects, such as reactions or pathways. | 6 |
SMRUCC.genomics.Assembly.MetaCyc.File.DataFiles
| Type | Summary | Members |
|---|---|---|
| Compounds | 该细胞系统中的所有的小分子化合物的集合，本集合取决于代谢网络的结构以及控制物质跨膜运输的蛋白质 | 2 |
| DataFile | All of the data file object in the metacyc database will be inherits from this class object type. | 11 |
| DNABindSites | This class describes DNA regions that are binding sites for transcription factors. | 0 |
| Enzrxns | Frames in the class Enzymatic-Reactions describe attributes of an enzyme with respect to a particular reaction. | 0 |
| Genes | Each frame in the class Genes describes a single gene, meaning a region of DNA that defines a coding region for one or more gene products. | 2 |
| Pathways | Frames in class Pathways encode metabolic and signaling pathways. | 0 |
| Promoters | Frames in this class define transcription start sites. | 1 |
| ProteinFeatures | Protein features (for example, active sites), This file lists all the protein features (such as active sites) in the PGDB. | 0 |
| Proteins | 本文件中列举出了所有的蛋白质复合物(CPLX)以及单体蛋白(MONOMER) | 1 |
| ProtLigandCplxes | The file lists all the complexes of proteins with small-molecule ligands in the PGDB. | 0 |
| Reactions | Frames within the Reactions class describe properties of a biochemical reaction independent of any enzyme or enzymes that catalyze that reaction. | 0 |
| Regulations | This class describes most forms of protein, RNA or activity regulation. | 1 |
| Regulons | This file lists all transcription factors in the PGDB and the genes that they regulate by binding upstream of the transcription unit containing those genes. | 0 |
| TransUnits | Frames in this class encode transcription units, which are defined as a set of genes and associated control regions that produce a single transcript. | 1 |
SMRUCC.genomics.Assembly.MetaCyc.File.DataFiles.DataTabular
| Type | Summary | Members |
|---|---|---|
| GeneLink | 在不同的数据库之间交换数据所需要的对象连接映射，即由PGDB中的Unique映射至通用基因号的关系对象 | 6 |
SMRUCC.genomics.Assembly.MetaCyc.File.DataFiles.Reflection
| Type | Summary | Members |
|---|---|---|
| FileStream | 8 | |
| MetaCycField | MetaCyc数据库中的一个对象的一个属性值 | 3 |
SMRUCC.genomics.Assembly.MetaCyc.File.DataFiles.Reflection.FileStream
| Type | Summary | Members |
|---|---|---|
| ReadingThread | 数据库并发读取线程委托 | 0 |
SMRUCC.genomics.Assembly.MetaCyc.File.DataFiles.Reflection.MetaCycField
| Type | Summary | Members |
|---|---|---|
| Types | Data field type in a Metacyc database object instance.(MetaCyc数据库中的一个对象实例的数据属性域的数据类型) | 6 |
SMRUCC.genomics.Assembly.MetaCyc.File.DataFiles.Slots
| Type | Summary | Members |
|---|---|---|
| BindReaction | Binding reaction between proteins and DNA binding sites such as promoters | 0 |
| Citation | Any of the above components may be omitted, but it is meaningless to supply a timestamp, curator or probability if the evidence-code is omitted. | 16 |
| Compound | The Class Compounds describe small-molecular-weight chemical compounds — typically, compounds that are substrates of metabolic reactions or compounds that activate or inhibit met… | 1 |
| DNABindSite | The class describes DNA regions that are binding sites for transcription factors. | 3 |
| Enzrxn | 7 | |
| Gene | 7 | |
| IComplexes | 复合物对象的接口 | 1 |
| Object | The object type is the base type of the objects definition both in the namespace PGDB.DataFile and PGDB.Schemas | 11 |
| Pathway | 16 | |
| Promoter | Frames in this class define transcription start sites. | 8 |
| Protein | The class of all proteins is divided into two subclasses: protein complexes and polypeptides. | 17 |
| ProteinFeature | This class describes sites of interest (such as binding sites, modification sites, cleavage sites) on a polypeptide. | 6 |
| ProtLigandCplxe | Protein-Small-Molecule-Complexes | 4 |
| Reaction | Reactions are organized into two parallel ontologies. | 10 |
| Regulation | This class describes most forms of protein, RNA or activity regulation. | 7 |
| TransUnit | Frames in this class encode transcription units, which are defined as a set of genes and associated control regions that produce a single transcript. | 3 |
SMRUCC.genomics.Assembly.MetaCyc.File.DataFiles.Slots.Protein
| Type | Summary | Members |
|---|---|---|
| IEnzyme | A general data structure of the enzyme entity that can catalyze a reaction.(能够催化酶促反应的酶分子的通用数据类型) | 4 |
SMRUCC.genomics.Assembly.MetaCyc.File.DataFiles.Slots.Regulation
| Type | Summary | Members |
|---|---|---|
| IRegulator | An object type that it has the ability to regulates the gene expression process. | 5 |
SMRUCC.genomics.Assembly.MetaCyc.File.FileSystem
| Type | Summary | Members |
|---|---|---|
| DatabaseLoadder | 当对MetaCyc数据库进行延时加载的时候，则需要使用到本对象进行数据的读取操作 | 18 |
| PGDB | The MetaCyc database file reader object. | 12 |
SMRUCC.genomics.Assembly.MetaCyc.File.TabularDataFiles
| Type | Summary | Members |
|---|---|---|
| Enzymes | (enzymes.col) For each enzymatic reaction in the PGDB, the file lists the reaction equation, up to 4 pathways that contain the reaction, up to 4 cofactors for the enzyme, up to… | 3 |
| Pathway | 代谢途径对象 | 3 |
| Pathways | (pathways.col) For each pathway in the PGDB, the file lists the genes that encode the enzymes in that pathway. | 3 |
SMRUCC.genomics.Assembly.MetaCyc.Schema
| Type | Summary | Members |
|---|---|---|
| DBLinkManager | MetaCyc database format dblink manager | 0 |
| EffectorMap | Regprecise Effector与MetaCyc Compounds Mapping | 0 |
| EquationEquals | 2 | |
| PropertyAttributes | 7 | |
| ProteinQuery | 1 |
SMRUCC.genomics.Assembly.MetaCyc.Schema.DBLinkManager
| Type | Summary | Members |
|---|---|---|
| DBLink | 与其他的数据库之间的外键链接 | 11 |
SMRUCC.genomics.Assembly.MetaCyc.Schema.Metabolism
| Type | Summary | Members |
|---|---|---|
| PathwayLink | 4 | |
| PathwayMappingTool | 使用一个汇总的MetaCyc数据库，根据目标物种的基因组以及蛋白质信息进行MetaCyc数据库的重建工作 | 3 |
| ReactionDirections | This slot specifies the directionality of a reaction. | 14 |
SMRUCC.genomics.Assembly.MetaCyc.Schema.PathwayBrief
| Type | Summary | Members |
|---|---|---|
| AssignGene | 将基因与相应的反应过程映射起来 | 4 |
| Pathway | 2 | |
| PwyFilters | 整理出代谢途径和相应的基因，对于基因个数少于5的代谢途径，其被合并至其他较大的SuperPathway之中去 | 1 |
SMRUCC.genomics.Assembly.MetaCyc.Schema.Reflection
| Type | Summary | Members |
|---|---|---|
| ExternalKey | 表示所标识的域为表与表之间的外键 | 4 |
| Path | ObjA ----> ObjB | 4 |
| PathRoute | 寻找MetaCyc数据库之中的任意两个对象之间的连接关系 | 3 |
SMRUCC.genomics.Assembly.MetaCyc.Schema.Reflection.ExternalKey
| Type | Summary | Members |
|---|---|---|
| Directions | 6 |
SMRUCC.genomics.Assembly.MetaCyc.Schema.TransportReaction
| Type | Summary | Members |
|---|---|---|
| CompoundSpecies | 1 |
SMRUCC.genomics.Assembly.MiST2
| Type | Summary | Members |
|---|---|---|
| Domain | The Microbial Signal Transduction database contains the signal transduction proteins for bacterial and archaeal genomes (2,457 complete and 5,181 draft). | 9 |
| MiST2 | MiST2对某一个基因组的注释所产生的数据库文件 | 1 |
| Replicon | 基因组之中的一个复制子 | 6 |
| Transducin | Signal Transduction Protein | 2 |
| TwoComponent | 6 | |
| WebServices | 2 |
SMRUCC.genomics.Assembly.NCBI.CDD
| Type | Summary | Members |
|---|---|---|
| Database | 9 | |
| DbFile | CDD database builder.(CDD数据库构建工具) | 5 |
| DomainInfo | The query interface of the local CDD database.(CDD数据库的查询接口) | 1 |
| Pn | 8 | |
| SmpFile | The file data structrue description of each domain smp description data before the CDD database compilation operation. | 3 |
SMRUCC.genomics.Assembly.NCBI.CDD.Blastp
SMRUCC.genomics.Assembly.NCBI.CDD.Database
| Type | Summary | Members |
|---|---|---|
| FastaLoader | 本对象会将读取的数据缓存与内存之中，以加速下一次查询的速度 | 0 |
SMRUCC.genomics.Assembly.NCBI.COG
| Type | Summary | Members |
|---|---|---|
| COGCategories | 10 | |
| COGFunction | COG function description data. | 2 |
| Function | 8 |
SMRUCC.genomics.Assembly.NCBI.COG.COGs
| Type | Summary | Members |
|---|---|---|
| COGFunc | fun2003-2014.tab Contains list of functional classes. | 4 |
| COGName | cognames2003-2014.tab Contains list of COG annotations. | 4 |
| COGProt | prot2003-2014.tab Contains RefSeq accession codes for all proteins with assigned COG domains. | 4 |
| COGs | 0. General remarks ############################################################ This Is a December 2014 release of 2003-2014 COGs constructed by Eugene Koonin 's group at the… | 2 |
| COGTable | cog2003-2014.csv CSV table row for COG, Contains list of orthology domains. | 10 |
| Genomes | genomes2003-2014.tab Contains list of genomes (711). | 5 |
| ProtFasta | prot2003-2014.fa.gz Sequences of all proteins with assigned COG domains in FASTA format (gzipped) The first word of the defline always starts with "gi|<protein-id>". | 1 |
SMRUCC.genomics.Assembly.NCBI.Entrez
| Type | Summary | Members |
|---|---|---|
| EntrezEntry | 查询某一个蛋白质或者基因对象所返回的结果数据下载入口点 | 0 |
| Genbank | The NCBI genbank data api handler | 2 |
| QueryHandler | http://www.ncbi.nlm.nih.gov/nuccore/?term= | 3 |
| TaxonomyWebAPI | Automatically Getting The Ncbi Taxonomy Id From The Genbank Identifier The question is whether, given a (long) list of Genbank identifiers, is possible to get the ncbi taxonom… | 3 |
SMRUCC.genomics.Assembly.NCBI.Entrez.ComponentModels
| Type | Summary | Members |
|---|---|---|
| I_QueryEntry | 用于表示获取查询结果的一个入口点 | 0 |
SMRUCC.genomics.Assembly.NCBI.GenBank
| Type | Summary | Members |
|---|---|---|
| Extensions | 8 | |
| gbExportService | Genbank export methods collection. | 11 |
| GBFFFeatureDumps | 3 |
SMRUCC.genomics.Assembly.NCBI.GenBank.CsvExports
| Type | Summary | Members |
|---|---|---|
| gbEntryBrief | Genbank数据库的简要信息Csv表格 | 3 |
| GenbankExportInfo | 2 | |
| Plasmid | tabular information about a plasmid replicate | 0 |
SMRUCC.genomics.Assembly.NCBI.GenBank.GBFF
| Type | Summary | Members |
|---|---|---|
| AssemblyLevelClassifier | Helper module for determines that the target genbank record is a complete assembled chromosome genome data or not. | 11 |
| AssemblyLevelEvidence | 组装水平判定结果的证据描述，用于日志输出与人工核查 | 5 |
| File | NCBI GenBank database file. | 17 |
| GbkParser | 2 | |
| GbkWriter | 将数据写入现有的genbank文件或者创建新的genbank文件 | 5 |
| GenomeAssemblyLevel | The genome assembly level of the target genbank record.(目标genbank记录所对应的基因组组装水平) | 10 |
| GenomeMolType | The molecule type of the target genbank record.(目标genbank记录所描述的分子的类型) | 18 |
| IgbComponent | Genbank数据库文件的构件 | 1 |
| MolTypeClassifier | A helper module for determines the molecule type of the target genbank record. | 14 |
| MolTypeEvidence | 分子类型判定结果的证据描述，用于日志输出与人工核查 | 5 |
SMRUCC.genomics.Assembly.NCBI.GenBank.GBFF.Keywords
SMRUCC.genomics.Assembly.NCBI.GenBank.GBFF.Keywords.FEATURES
| Type | Summary | Members |
|---|---|---|
| CDS | 为CDS字段记录所特化的对象 | 1 |
| Feature | A sequence feature site on the genome DNA sequence. | 10 |
| FeatureQualifiers | Qualifiers provide additional information about features. | 67 |
| FEATURES | 7 | |
| Location | 5 | |
| ParserHelper | 2 | |
| RegionSegment | A site region on the sequence. | 4 |
| SearchInvoker | 可以使用本模块内的方法搜索FEATURES模块之中的内容 | 2 |
| tRNAAnticodon | 0 |
SMRUCC.genomics.Assembly.NCBI.GenBank.TabularFormat
| Type | Summary | Members |
|---|---|---|
| DbAPI | 4 | |
| ProteinDescription | tabular data model for protein data information | 6 |
| PTT | The brief information of a genome.(基因组的摘要信息) | 17 |
| PTTDbLoader | 11 | |
| PTTEntry | 数据库文件的列表 | 14 |
| PTTFileReader | 1 | |
| Rpt | 2 |
SMRUCC.genomics.Assembly.NCBI.GenBank.TabularFormat.ComponentModels
| Type | Summary | Members |
|---|---|---|
| GeneBrief | The gene brief information data in a ncbi PTT document.(PTT文件之中的一行，即一个基因的对象摘要信息) | 9 |
SMRUCC.genomics.Assembly.NCBI.GenBank.TabularFormat.FastaObjects
| Type | Summary | Members |
|---|---|---|
| GeneObject | .ffn 基因序列 | 0 |
| GenomeSequence | .fna 基因组序列 | 0 |
| Protein | .faa 蛋白质序列 | 0 |
SMRUCC.genomics.Assembly.NCBI.SequenceDump
| Type | Summary | Members |
|---|---|---|
| NTheader | The fasta header of the nt database. | 8 |
| Nucleotide | NCBI genbank title format fasta parser | 1 |
| Protein | NCBI genbank title format fasta parser | 0 |
SMRUCC.genomics.Assembly.NCBI.Taxonomy
| Type | Summary | Members |
|---|---|---|
| Accession2Taxid | 将序列的AccessionID编号转换为Taxid编号 | 10 |
| AccessionTaxID | database for Accession2Taxid | 1 |
| DmpFileReader | 1 | |
| names | Taxonomy names file (names.dmp): + tax_id -- the id of node associated with this name + name_txt -- name itself + unique name -- the unique Variant Of this name If name Not un… | 7 |
| NcbiTaxonomyTree | Builds the following dictionnary from NCBI taxonomy nodes.dmp and names.dmp files json { Taxid : namedtuple('Node', ['name', 'rank', 'parent', 'children'] } + https://… | 27 |
| Ranks | 将物种分类节点按照分类等级进行分组 | 4 |
| TaxidMaps | 5 | |
| TaxiValue | 7 | |
| Taxonomy | Build Taxonomy tree from NCBI genbank data. | 3 |
| TaxonomyExtensions | 1 | |
| TaxonomyNode | The tree node calculation model for NcbiTaxonomyTree, a labeled tree node for a specific ncbi taxid. | 6 |
| TaxonomyWeb | The Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases. | 2 |
| TaxonValue | 2 |
SMRUCC.genomics.Assembly.NCBI.Taxonomy.TaxidMaps
| Type | Summary | Members |
|---|---|---|
| Mapping | 将所给定的编号映射为taxid的一个操作 | 3 |
SMRUCC.genomics.Assembly.Uniprot
| Type | Summary | Members |
|---|---|---|
| FastaHeader | 7 | |
| IdMapping | idmapping_selected.tab We also provide this tab-delimited table which includes the following mappings delimited by tab 1. | 22 |
| UniprotFasta | A fasta object which is specific for the uniprot fasta title parsing.(专门用于解析Uniprot蛋白质序列记录的Fasta对象) The following is a description of FASTA headers for UniProtKB (including alte… | 3 |
SMRUCC.genomics.Assembly.Uniprot.Web
| Type | Summary | Members |
|---|---|---|
| Entry | tabular export of the protein list in tsv format | 26 |
| Formats | 20 | |
| ID_types | 194 | |
| Retrieve_IDmapping | 7 | |
| WebServices | https://www.uniprot.org/help/api_queries https://www.uniprot.org/help/text-search https://www.uniprot.org/help/query-fields | 2 |
SMRUCC.genomics.Assembly.Uniprot.XML
| Type | Summary | Members |
|---|---|---|
| citation | 9 | |
| comment | 3 | |
| dbReference | 2 | |
| entry | Describes a UniProtKB entry. | 7 |
| Extensions | 8 | |
| feature | Describes different types of sequence annotations. | 5 |
| featureTypes | Describes the type of a sequence annotation. | 39 |
| gene | Describes a gene. Equivalent to the flat file GN-line. | 3 |
| GetIDs | 1 | |
| location | Describes a sequence location as either a range with a begin and end or as a position. | 6 |
| molecule | Describes a molecule by name or unique identifier. | 2 |
| position | 序列上面的某一个位点位置 | 4 |
| protein | Describes the names for the protein and parts thereof. | 5 |
| reaction | 3 | |
| recommendedName | 1 | |
| sequence | the protein sequence data | 7 |
| UniProtXML | Describes a collection of UniProtKB entries, XML file can be download from the uniprot database id mappings result. | 7 |
| value | 一条值数据记录 | 1 |
SMRUCC.genomics.Assembly.Uniprot.XML.GetIDs
| Type | Summary | Members |
|---|---|---|
| IDTypes | 8 |
SMRUCC.genomics.Assembly.Uniprot.XML.UniRef
| Type | Summary | Members |
|---|---|---|
| entry | http://uniprot.org/uniref | 0 |
SMRUCC.genomics.ComponentModel
| Type | Summary | Members |
|---|---|---|
| IExpressionValue | interface for molecule feature expression value in one sample | 0 |
| MimeTypes | 9 | |
| TabularLazyLoader | NCBI PTT和MetaCyc数据库所公用的多文件的数据库加载器的基本类型 | 1 |
SMRUCC.genomics.ComponentModel.Annotation
| Type | Summary | Members |
|---|---|---|
| CatalogList | a [term => id()] tuple data | 3 |
| CatalogProfile | a wrapper of Dictionary | 3 |
| CatalogProfiles | a numeric profile data | 1 |
| CatalogProfiling | a level 1 class dataset | 1 |
| ClassProfiles | ID class counter | 0 |
| ECNumber | Enzyme Commission Number | 15 |
| EnzymeClasses | The enzyme types enumeration. | 16 |
| EnzymeQuery | EC number query helper | 2 |
| GeneTable | The gene dump information from the NCBI genbank. | 7 |
| IBlastHit | A simple alignment annotation result model | 3 |
| ICOGCatalog | 这个基因的注释结果之中除了COG编号之外，还有这个编号所属的COG分类 | 1 |
| IEnzymeObject | 1 | |
| IFeatureDigest | The feature annotation data of the genes. | 1 |
| IGeneBrief | The basically information of a gene object. | 2 |
| IQueryHits | the annotation alignment result model with score value | 1 |
| PathwayBrief | An abstract biological pathway model | 6 |
SMRUCC.genomics.ComponentModel.Chemical
| Type | Summary | Members |
|---|---|---|
| FormulaData | The formula composition data model | 9 |
| PeriodicTable | 元素周期表 | 4 |
SMRUCC.genomics.ComponentModel.DBLinkBuilder
| Type | Summary | Members |
|---|---|---|
| DBLink | Database xref data | 4 |
| DBLinksManager | 1 | |
| IDBLink | 3 | |
| SecondaryIDSolver | This module ensure that all of the id is main id, not secondary id. | 8 |
| Synonym | data alias model, a mapping of the main accession id to a collection of the secondary accession id. | 3 |
SMRUCC.genomics.ComponentModel.EquaionModel
| Type | Summary | Members |
|---|---|---|
| Equation | 10 | |
| EquationBuilder | 3 | |
| Equivalence | 1 | |
| ICompoundSpecies | A metabolite compound abstract model which contains the unique reference id of the metabolite and the chemical factor to current equation | 1 |
| IEquation | 2 | |
| Reaction | A general reaction model | 3 |
| ReactionDirection | Represents the direction of a reaction | 6 |
SMRUCC.genomics.ComponentModel.EquaionModel.DefaultTypes
| Type | Summary | Members |
|---|---|---|
| CompoundSpecieReference | the compound model reference. | 1 |
| Equation | 默认类型的反应表达式的数据结构，可以使用EquationBuilder.CreateObject())来进行构建 | 1 |
SMRUCC.genomics.ComponentModel.Loci
| Type | Summary | Members |
|---|---|---|
| Extensions | 1 | |
| IMotifScoredSite | This motif site have the scoring calculation value | 1 |
| IMotifSite | Motif site model on both DNA/RNA and protein sequence. | 2 |
| Location | A location property on a sequence data. | 14 |
| Loci | 带标签的位置信息，只不过这个位点的位置信息是展开的 | 4 |
| LociAPI | The extension method for the location object operations. | 3 |
| LocusExtensions | Methods for some nucleotide utility. | 8 |
| MotifSite | 带标签的位点信息，只不过这个位点的位置信息是构建好的 | 1 |
| NucleotideLocation | Loci segment location information on an nucleotide sequence, this object added an NucleotideLocation.Strand information on Location data. | 22 |
| NucleotideLocationParser | Custom parser for csv field | 0 |
| Position | 百分比相对位置 | 3 |
| SegmentRelationships | The location relationship description enumeration for the two loci sites on the nucleotide sequence. | 14 |
| Strands | The direction of this segment on the nucleotide sequence. | 6 |
SMRUCC.genomics.ComponentModel.Loci.Abstract
| Type | Summary | Members |
|---|---|---|
| IContig | Abstract model with location data. | 0 |
| ILocationComponent | This type of the object has the loci location value attribute. | 1 |
| ILocationSegment | 2 | |
| ILoci | 只有左端起始位点的模型对象 | 1 |
| ITagSite | This loci site have a tag | 2 |
| TagSiteExtensions | 1 |
SMRUCC.genomics.ContextModel
| Type | Summary | Members |
|---|---|---|
| Context | Context model of a specific genomics feature site. | 14 |
| Density | Genomics context relative abundance | 3 |
| Extensions | 1 | |
| GenomeContext | 表示一个基因组上下文模型，用于在内存中高效地存储、索引和查询基因组特征（如基因）。 | 31 |
| GenomeContextProvider | 基因组上下文计算工具，一般使用PTT或者GFF文件作为数据源. | 7 |
| IGenomicsContextProvider | 3 | |
| LocationDescriptions | 6 | |
| RelationDelegate | The working core of the genomics context provider. | 2 |
| Relationship | 描述位点在基因组上面的位置，可以使用Relationship.ToString()函数获取得到位置描述 | 3 |
| TFDensity | Calculates the relative density of the TF on each gene on the genome. | 3 |
SMRUCC.genomics.ContextModel.Promoter
| Type | Summary | Members |
|---|---|---|
| Extensions | 3 | |
| PromoterRegionParser | 直接从基因的启动子区选取序列数据以及外加操纵子的第一个基因的启动子序列 | 3 |
SMRUCC.genomics.MetabolicModel
| Type | Summary | Members |
|---|---|---|
| MetabolicCompound | internal standard model of the metabolite object | 0 |
| MetabolicPathway | 通路信息（用于通路级别汇总） | 2 |
| MetabolicReaction | A unify reaction model in the GCModeller system | 3 |
SMRUCC.genomics.Metagenomics
| Type | Summary | Members |
|---|---|---|
| BIOMTaxonomy | 9 | |
| BIOMTaxonomyParser | Parser and stringfier of Taxonomy object. | 3 |
| GenomeNameIndex | in-memory name search | 2 |
| LCA | LCA（最低公共祖先）算法 | 6 |
| LcaResult | LCA计算结果 | 5 |
| OTUData | OTUData.data that associated with OTUData.OTU tag | 4 |
| SampleAbundanceSelector | 2 | |
| Taxonomy | A simple organism taxonomy model. | 18 |
| TaxonomyExtensions | 4 | |
| TaxonomyRanks | the organism taxonomy rank levels | 16 |
SMRUCC.genomics.ObjectQuery
| Type | Summary | Members |
|---|---|---|
| IQueryExtensions | Extensions for object query in the GCModeller biological components | 3 |
SMRUCC.genomics.ProteinModel
| Type | Summary | Members |
|---|---|---|
| DomainModel | The simple protein domain motif model. | 0 |
| DomainObject | Domain identifier + Domain Location | 2 |
| IMotifDomain | 一个蛋白质结构域对象的抽象模型 | 2 |
| Protein | A type of data structure for descript the protein domain architecture distribution.(一个用于描述蛋白质结构域分布的数据结构) | 5 |
SMRUCC.genomics.ProteinModel.ChouFasmanRules
| Type | Summary | Members |
|---|---|---|
| AminoAcid | 8 | |
| ChouFasman | The Chou-Fasman method is a bioinformatics technique used for predicting the secondary structure of proteins. | 6 |
| ChouFasmanParameter | 37 | |
| SecondaryStructures | 蛋白质的二级结构分类 | 8 |
SMRUCC.genomics.ProteinModel.ChouFasmanRules.Rules
| Type | Summary | Members |
|---|---|---|
| RuleAlphaHelix | 1 | |
| RuleBetaSheet | 1 | |
| RuleBetaTurn | 1 | |
| RuleOverlap | 1 |
SMRUCC.genomics.SequenceModel
| Type | Summary | Members |
|---|---|---|
| BioSequenceValidator | 5 | |
| Bits | Sequence model in bytes | 8 |
| IPolymerSequenceModel | Sequence model for a macro biomolecule sequence. | 1 |
| ISequenceBuilder | This class can be using for build a FastaSeq object. | 3 |
| ISequenceModel | The biological sequence molecular model. | 5 |
| KSeqCartesianProduct | kmer sequence generator | 1 |
| MolecularWeightCalculator | 核酸链或者多肽链分子的相对分子质量的计算工具 | 15 |
| SeqTypes | 8 | |
| TypeExtensions | Extensions helper function for different type of bio-sequence. | 13 |
SMRUCC.genomics.SequenceModel.FASTA
| Type | Summary | Members |
|---|---|---|
| Extensions | 2 | |
| FastaFile | A FASTA file that contains multiple sequence data. | 20 |
| FastaSeq | The FASTA format file of a bimolecular sequence.(Notice that this file is only contains on sequence.) | 29 |
| HeaderFormats | Fasta序列在不同的数据库之中的标题的格式的帮助函数模块 | 4 |
| IAbstractFastaToken | The fasta object is a sequence model object with a specific title to identify the sequence and a sequence data property to represents the specific molecule. | 2 |
| IFastaProvider | A fasta sequence data provider | 2 |
| ISequenceProvider | This object could provide a biological sequence data through ISequenceProvider.GetSequenceData() function. | 1 |
| StreamIterator | 流式 FASTA 读取器：逐条读取，内存占用恒定（仅当前序列）。读取超大型的fasta文件所需要的一个数据对象 | 12 |
| StreamWriter | A fasta stream writer, apply for write a huge fasta seqnce collection | 0 |
SMRUCC.genomics.SequenceModel.FASTA.Reflection
| Type | Summary | Members |
|---|---|---|
| FastaAttributeItem | 4 | |
| FastaExportMethods | 對象模塊將數據庫中的一條記錄轉換為一條FASTA序列對象 | 8 |
| FastaObject | 用於類型定義上的FASTA序列對象的標題格式 | 3 |
| FastaSequenceEntry | 自定義屬性用於指示哪一個屬性值為目標對象的序列數據 | 0 |
SMRUCC.genomics.SequenceModel.NucleotideModels
| Type | Summary | Members |
|---|---|---|
| Assembly | 3 | |
| Bases | 2 | |
| ChunkedNtFasta | 分块存储的FASTA序列对象，用于处理大型基因组序列，例如植物基因组，动物基因组这些序列长度超过了2GB的基因组序列 | 9 |
| Contig | a model for nucleotide sequence region on genomics sequence | 3 |
| Conversion | 转换包含有普通类型的基本碱基字符，还包括有简并碱基字符 | 8 |
| DegenerateBasesExtensions | 简并碱基 简并碱基是根据密码子的兼并性,常用一个符号代替某两个或者更多碱基。 根据密码子的兼并性,常用一个符号代替某两个或者更多碱基。例如，编译丙氨酸的 可以有4个密码子GCU\GCC\GCA\GCG,这时生物学上为了方便，用字母N指代UCAG 四个碱基，故说编译丙氨酸的密码子是GCN，其中N就是简并碱基。 通常生物学上根据蛋白质序列设计引… | 4 |
| DNA | Deoxyribonucleotides NT base which consist of the DNA sequence. | 32 |
| Extensions | 7 | |
| mRNA | 1 | |
| NucleicAcid | The nucleotide sequence object.(核酸序列对象) | 19 |
| NucleicAcidStaticsProperty | NucleicAcid sequence property calculator | 11 |
| SegmentObject | 片段数据，包含有在目标核酸链之上的位置信息以及用户给这个片段的自定义的标签信息 | 7 |
| SimpleSegment | 没有更多的复杂的继承或者接口实现，只是最简单序列片段对象 | 8 |
SMRUCC.genomics.SequenceModel.NucleotideModels.Translation
| Type | Summary | Members |
|---|---|---|
| Codon | 密码子对象 | 14 |
| GeneticCodes | http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=tgencodes#SG25 | 37 |
| NtHelper | 1 | |
| TranslationTable | transl_table=1 标准密码子表 | 4 |
| TranslTable | Compiled by Andrzej (Anjay) Elzanowski and Jim Ostell at National Center for Biotechnology Information (NCBI), Bethesda, Maryland, U.S.A. | 14 |
| TranslTableTextReader | 1 |
SMRUCC.genomics.SequenceModel.Patterns
| Type | Summary | Members |
|---|---|---|
| IPatternSite | 3 | |
| PatternModel | 一个经过多序列比对对齐操作的序列集合之中所得到的残基的出现频率模型，可以用这个模型来计算突变率以及SNP位点 | 1 |
| PatternsAPI | 7 | |
| SimpleSite | 1 |
SMRUCC.genomics.SequenceModel.Patterns.Clustal
SMRUCC.genomics.SequenceModel.Patterns.Variation
| Type | Summary | Members |
|---|---|---|
| Variations | 18 |
SMRUCC.genomics.SequenceModel.Polypeptides
| Type | Summary | Members |
|---|---|---|
| AminoAcid | Enumerates all of the 20 amino acids. | 46 |
| AminoAcidObjUtility | 22 | |
| Polypeptide | Protein polypeptide sequence. | 8 |
SMRUCC.genomics.SequenceModel.Slicer
| Type | Summary | Members |
|---|---|---|
| CutSequence | Cut sequence for DNA/protein | 8 |
| GenBankSlicer | slicer for the ncbi genbank origin sequence, which is stored in the GBFF file, this slicer can be used to cut a specific sequence region from a genbank sequence file | 1 |
| ISlicer | A wrapper of the biological sequence region cutter, which can be used to cut a specific sequence region from a FASTA sequence or a chunked FASTA sequence | 3 |
| KSeq | k-mer sequence model | 8 |