SPINE 2: A System for Collaborative Structural Proteomics within a Federated
Database Framework
Chern-Sing Goh1#, Ning Lan1#, Nathaniel Echols1#, Shawn Douglas1,
Duncan Milburn1, Paul Bertone2, Tom Acton3, Deyou Zheng3, Zeba Wunderlich3, Gaetano T. Montelione3, and Mark Gerstein1,4*
The current Spine (1.5) can be found at https://www.doczj.com/doc/eb4837664.html,/spine/ and the new Spine (2.0) is at https://www.doczj.com/doc/eb4837664.html,/spine/.
The older spine https://www.doczj.com/doc/eb4837664.html,/nesgc/summary.cgi (1.0).
1 Molecular Biophysics and Biochemistry
2 Molecular, Cellular, and Developmental Biology
4 Computer Science
Yale University
266 Whitney Ave
New Haven, CT 06520
3 Center for Advanced Biotechnology and Medicine
Rutgers University
Piscataway, NJ 08854
#These authors contributed equally to this work.
02-15-03
*corresponding author: mark.gerstein@https://www.doczj.com/doc/eb4837664.html,
Abstract
We present version 2 of the SPINE system for structural proteomics. SPINE is available over the web at https://www.doczj.com/doc/eb4837664.html,. It serves as central hub for the Northeast Structural Genomics Consortium, allowing collaborative experimentation to be carried out in a distributed fashion. The core of SPINE is a laboratory information management system (LIMS) for information related the progress of the consortium in cloning, expressing and purifying proteins and then solving their structures by NMR or X-ray crystallography. Originally, SPINE focused on tracking constructs, but, in its current form, it is able to track target sample tubes and store detailed sample histories. The central database comprises a set of standard relational tables and data dictionary that form a preliminary ontology for proteomic properties and provide a framework for large-scale data mining. Moreover, SPINE functions within a federation of interoperable information resources. These can be divided into (i) local resources closely coupled with SPINE that enable it to handle less standardized information (e.g. integrated mailing and publication lists), (ii) other information resources in the NESG consortium that are inter-linked with SPINE (e.g. crystallization LIMS local to particular laboratories), and (iii) international archival resources that SPINE shares links and information with (e.g. TargetDB at the PDB). Introduction
The structural genomics effort is generating a vast amount of data, underscoring the need for database systems and servers that can organize this information (1-4). Structural genomics consortia have been formed to consolidate these efforts. These consortia, including the Northeast Structural Genomics Consortium (NESG), are composed of numerous researchers in disparate locations working cooperatively at each step of the structural determination process, from selection of targets through to analysis of the results. The SPINE (Structural Proteomics In the NorthEast) database (5) was designed to coordinate the efforts of these researchers in the NESG as an information management and data analysis resource.
SPINE was created in 1999 as a data repository with associated data-mining tools. Through many revisions, its tracking functionality has expanded to accommodate detailed histories for individual samples, thereby presenting a more complete framework for transmitting information through all stages in high-throughput protein production and structure determination. In the original publication, Bertone et al.described the system architecture and how it was interlinked with specific tools to enable data-mining. There have been previous discussions regarding a role of proteomics ontologies in structural genomics (6) and at this stage, SPINE can be described as the beginning of an ontology of standardized protein properties. Here we present version 2 of SPINE and describe its overall development over the last three years.
Our system encompasses several aspects. Firstly, the core of the SPINE system (core
SPINE) is a centralized information management system, which tracks protein targets through the structure determination process, from the cloning of expression constructs to final structural characterization and submission of PDB coordinate sets, providing histories for particular samples. Secondly, SPINE sits at the center of a federation of computational resources; there are a number of SPINE-integrated web tools, both local and remote, that allow members of the consortium to post further information related to protein targets. Finally, the database can be analyzed retrospectively to identify factors that contribute to the ease with which individual proteins may be studied. Although the system is tailored to the needs and goals of the NESG, we expect that many of its features could be readily adapted to similar projects.
Implementation of Core SPINE System
The core database is implemented in MySQL on a Unix platform, with its user interface written entirely in the Perl programming language and integrated with the Apache web server. (Previous versions of the database used PHP extensively;the current implementation provides a more consistent platform.) This approach offers a considerable speed advantage and allows sharing of libraries with offline programs used in the development of future releases and associated tools. Perl's suitability for systems programming also allows a wide variety of other modules to be used in the server with minimal setup and administrative overhead, such as the BLAST package (7), Java, and Lisp code for data analysis. The core data elements are stored in a number of tables that record the experimental progress of individual targets (Figure 1). Auxiliary tables control access to the database and record a history of individual changes.
Initially, the basic unit tracked by SPINE was the expression construct. However, with the evolution by the NESG consortium of a systematic protein target selection process (8), these protein targets, each of which may have multiple associated constructs, have been made the focus of the database. All derivative records from the target onwards comprise one-to-many relationships. At the level of protein purification, we have introduced parent-child relationships for individual protein samples, broadening the data structure instead of compressing multiple purification records into a single instance. Most records include some form of unstructured data, often in the form of analytical images that have been uploaded to the server. This has even been extended to encompass email (see below) related to specific targets.
A key feature of the database is the ability of any registered member of the consortium to add and modify entries via an intuitive web interface. This is regulated by journaling all changes to data (and the user responsible), and by restricting access to certain entries. More flexible and customized methods of data entry are also possible. The use of direct SQL and the Open Database Connectivity (ODBC) protocols enable a variety of remote interfaces to the server (such as Excel spreadsheets or Java programs), and data interchange uses standard XML or table formats. These features enable bulk uploading of local datasets into SPINE. In the future, development will focus mainly on the
schema, the SPINE data dictionary, and display functions, leaving data entry at the prerogative of individual users
Integration of Core SPINE with a Federation of other Resources
The core SPINE database system sits at the center of a federation of information resources diagrammed in Figure 2.The core of SPINE is a relational database handling highly standardized information that interoperates with a set of local resources designed to handle more heterogeneous data that is not readily stored in tables. Some of these features include the incorporation of free text fields, the ability to upload data files, and the utility of its data mining tools and servers.
SPINE is also associated with external resources that are coupled together in a loose federation associated with the NESG. These resources can be categorized into three tiers.
1. Local Integrated Resources
SPINE is integrated with a number of "local" resources, resident on the same machine and tightly coupled to it. These include:
a.The NESG website. This is built around a wiki platform, allowing for easy remote
editing of such things as links to related projects.
b. A Structure Gallery. This is used for displaying completed 3D structures of protein
targets.
c.Publication page. This is built on elaborating the NCBI PubMed XML dump to
incorporate such things as targets and websites. It allows the direct cross-referencing of targets, URLs, and medline identifiers.
d.The Target Info Bulletin Board. The idea behind this is there is a lot of information
that people would like to track about a particular target that does not fit into
standardized tables. This can be easily sent in the form of simple email messages that are cc'ed to this bulletin board. These messages are automatically parsed for specific target identifiers, and each instance of a target identifier in the archive is linked to its corresponding record in SPINE and vice versa.
2. Other NESG Resources
There are a number of other computational resources that are part of the NESG project which are connected to SPINE. In particular, the diverse needs of experimentalists have led to the creation of several specialized databases within the consortium, dedicated to aspects of the project such as NMR data collection or crystal screening that are not well-
served by a single central resource. SPINE is currently being extended to facilitate storage of summary information from these satellite databases and even perform remote queries. Some of the resources that SPINE interoperates with are the PEP (9) cluster viewer at Columbia University and ZebaView target list at Rutgers University where new target entries are automatically downloaded nightly and inserted into SPINE. Other web resources SPINE is linked with include the SPINS database at Rutgers (17), the PartsList and Gene Census databases at Yale University (18), the Proteus crystallization database at Columbia University, and a LIMS system at the University of Toronto.
3. External Archival Resources
SPINE is also connected to resources outside of the NESG through an evolving portal portal called SmartLink. This system handles much of the difficulty translating ORF and structure identifiers and dealing with missing or dangling links. Most of the information pertaining to 3D structure determinations is transferred to the PDB (13). Other resources that SPINE is connected to include are SwissProt (10), PIR (11), BMRB (12), TargetDB (13)- the RCSB’s registry for structural genomics projects - and Wormbase (14). Detailed sample tracking and history
The requirements of tracking a target’s progress across multiple institutions include the ability to maintain a list of individual samples and their locations. For example, a protein may be purified at one site, shipped to another for crystallization screening, and then sent to a third site for structural characterization. Protein production requires greater flexibility, since not only protein samples but construct stocks and fermentation batches must be stored and tracked. The current system handles all sample types via tube records, whose contents are determined from their “parent” record (construct, expression, or purification). Each “sample tube” generated in the pipeline of sample production is assigned a unique tube identifier, which eventually will be mapped into a bar coding system. Therefore, a collection of protein samples may be assigned for biophysical analysis without regard for their specific target, since the database automatically determines their history based on tube identifier. This concept has been extended to handle sample plates, which behave as an aggregation of tube records identified by their well number.With this approach, information pertaining to shipments as well as physical location can be easily associated with sample records. This provides accounting of material transfer between institutions, and a more accurate picture of the progress of individual targets.
Discussion
In this paper we’ve described the SPINE version 2, a relational database system that that serves as the LIMS for the NESG consortium. This new version serves as the center of a
federation of inter-operable resources to allow for distributed functionality across the entire consortium. The major goals of the database system include:
1. A distributed LIMS
Constructing a distributed LIMS enables information to be shared among all the members of the consortia. From a vast number of local and external resources, SPINE can incorporate and process data, which can then be made accessible through a simple user browser interface at any location.
2. Standardized proteomics ontology
An improved representation of protein properties that is standardized will allow for more efficient retrospective analysis of structural and functional information, which can be mined using an incorporated generalized data mining web tool.
3. Datamining
The schema for SPINE has been designed to facilitate analysis of the collected data to further optimize target selection criteria. Bertone et al (5)demonstrated the potential data-mining capabilities of the SPINE database by developing a decision tree algorithm that was used to infer whether a protein was soluble, and which biochemical properties contributed most to solubility, from a dataset of 562 M. thermoautotrophicum protein expression constructs. The decision tree analysis indicated that protein characteristics such as protein length, hydrophobicity, and percent composition of charged residues were the strongest determinants in inferring the solubility of a protein.At present, the number of targets in the NESG is 5388, roughly 10 times the size of the original dataset, and presents a wealth of new information for mining (Goh et al., in preparation).
Future Directions in interoperation
We envision enhancing the integration with other databases by establishing a tighter interoperation with external databases, particularly those in the second tier.
To this end, we are currently investigating automatic data integration tools to span our heterogeneous federation of databases into what appears as a single (but virtual) database. Such an approach seems like a logical progression since not only does it remove implementation dependencies for each site, but it also manages the interconnections between sites. Users at different project locations and people from the outside could then interface, query, and interact with the uniform interface at a single site, rather than considering the details of all the different lab databases. This will allows us to adopt a hub and spoke topology of database connections rather than a fully interconnected network, simplifying the interface as compared to an all-with-all federation. It also provides a graceful transition from a very loose federation to a single unified database.
A number of technologies that may be useful in this include the SDSC Storage Resource Broker (SRB, https://www.doczj.com/doc/eb4837664.html,/DICE/SRB, a piece of client-server middleware that
provides a uniform interface for connecting to heterogeneous data resources over a network and accessing replicated data sets), Bio-Kleisli (15), and the Object-Protocol Model (16).
Obtaining the software
The complete code for SPINE, including table creation commands, may be downloaded by arrangement with the authors.
Acknowledgements
We thank Michael Baran, Natalia Denissova, Chi Kent Ho, LiChung Ma, and Rong Xiao for helpful discussions.
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Figure 1
Schema of the SPINE database, showing evolution of tables and data flow. (A) The original version of SPINE, in which the construct was the primary object tracked, and table records typically had one-to-one relationships. (B) Current schema. Experimental records (outlined in blue) all have one-to-many relationships branching from target entries. The most recent additions to the database are highlighted in red.
Figure 2
Overview of the SPINE federation.
Figure 3
Assorted screenshots from the NESG/SPINE web server; (a) the
NESG home page, providing links to all the institutions involved and to
the gallery of structures produced by them; (b) the SPINE target summary
page showing the data recorded in SPINE at each stage of the protein
production and structure determination process (blue shading indicates
data is present) for every target in the project; (c) one of the new
additions in version 2 of SPINE is the ability to track in detail a given sample tube down to a well, plate and physical location and can be changed by clicking on the desired sample entry (blue circle).
Lesson 1 你要举办一个生日聚会吗？ Let’s talk L：今天是星期几？ T：是星期三。 L：我的生日就要到了。 T：你的生日是什么时候？ L：下周日。 T：你要举办一个生日聚会吗？ L：是的，我要。下周日晚上我要在家里举办一个生日聚会。你想要来吗？ T：当然，我想去。你会叫伊芙来吗？ L：当然。 Let’s make 亲爱的王菲： 这个周日我要在我家举办一个生日聚会。请在晚上6点来参加这个聚会。 Lulu Read and write 我是佩格。明天是周日。首先，上午我要做作业。接下来，我要打扫我的房间。然后，下午我要去看望奶奶。最后，晚上我要在家里看电视。 Make and say 一个假期计划 劳动节就要来了。 你们要做什么呢？ 请告诉我你们的计划。 五月一日，我要去拜访我的朋友。 五月二日，我要去上游泳课。 五月三日，我要帮妈妈洗衣服。
Read 爸爸的生日聚会 我是玛丽。今天是我爸爸的生日。天气很好，阳光灿烂。我们要为他举办一个生日聚会。现在我正在和妈妈一起购物。 我要买些水果。妈妈要买些鸡蛋。她要给爸爸做个生日蛋糕。 聚会将在4点钟开始。现在是1点钟，我在询问我的叔叔和阿姨是否能够来参加这个聚会。“嗨，露西阿姨！今天是我爸爸的生日，你想来参加他的生日聚会吗？”“哦，我想去。可今天也是蒂姆的生日，我可以带他一起去这个聚会吗？” “您当然可以。顺便问一句，谁是蒂姆啊？”“哈哈，蒂姆是我的小狗。” Lesson 2 你明天要做什么？ Let’s talk E：你明天要做什么？ D：我要去购物。 E：你要买什么？ D：我要买一张中国地图。 E：我想买些蜡笔。我能和你一起去吗？ D：当然可以！ E：我们怎么去呢？ D：骑自行车，可以吗？ E：好的。 Make and say 你这周六要做什么？ 我要去看电影。
The way 的用法 Ⅰ常见用法： 1)the way+ that 2)the way + in which（最为正式的用法） 3)the way + 省略（最为自然的用法） 举例：I like the way in which he talks. I like the way that he talks. I like the way he talks. Ⅱ习惯用法： 在当代美国英语中，the way用作为副词的对格，“the way+ 从句”实际上相当于一个状语从句来修饰整个句子。 1)The way =as I am talking to you just the way I’d talk to my own child. He did not do it the way his friends did. Most fruits are naturally sweet and we can eat them just the way they are—all we have to do is to clean and peel them. 2）The way= according to the way/ judging from the way The way you answer the question, you are an excellent student. The way most people look at you, you’d think trash man is a monster. 3）The way =how/ how much No one can imagine the way he missed her. 4）The way =because
课题：Lesson1 Whose watch is it? 1 课时 教学内容：词汇 教学目标： 1. 理解并掌握形容词性物主代词。 2. watch 、whose 、his 、等黑体单词要能听懂，会说会认读并会拼写。 3. very much 、Here you are 能听懂，会说，会认读 教学重点：要会使用形容词性物主代词your、my 、our 、his 、her 、their 这几个单词。 教学难点：单词在实际语境中的运用。 教学用具：录音机、卡片。 教学过程： 一、复习以前学过的形容词性物主代词，教师出示单词卡片。看单词说汉语，看汉语说单词。 Your my her our their 你的我的 她的我们的他们的 二、导入新课学单词： watch 、whose 、his、think 、ask、very 、much 、man 、beautiful 、remember A. 教师根据元音字母在单词中的发音规律讲解单词读音。 B. 学生试读单词。 C. 学生听录音并跟读单词。 D. 学生分组读单词，互相纠正单词发音。 E、学生站起来读单词，教师纠正学生发音。 F、学生熟读并记忆单词。 三、操练反馈：教师发给学生每人一张纸条，上面只有英文没有中文，给学
生一两分钟时间，让他们快速写出中文。精品文档
四、布置作业：熟读并记忆单词。 本课单词带音标写三遍。 2 课时 教学内容：Let 's learn 教学目标：理解和掌握whose 的用法教学重点、难点： Whose watch is it? It 's his watch. Is this your watch? Oh, yes. It 's my watch. Here you are. Thank you very much. 教学方法：听、说、演。 教学用具：录音机、图片。 教学过程： 一、复习检查本课所学单词。 二、导入新课 A、教师那一本书介绍：This is my book. 教师问：Whose book is this? 学生 回答：It's your book. 教师在教室里随机拿学生物品问：whose …is this 学生用句式、It' ................ 来回答。 B 、教师简笔画卡片带单词： My wahch ；Your clock; his basket ；her cups ； Our glasses；their bags；. 学生看卡片单词用：
科普版小学六年级上册复习题习题：选择 1.His father always _____ him toschool at 8:00. A. takes B. to take C. take Amy_____ TV in the evening. A. watch B. watching C. watches never_____ the floor. A. mop C. mops always_____ breakfast at 7:00. A. make B. makes C. making ， shealways _____ sports at 9:00. A. does B. do 习题： you have English class every day A. Do B. Are C. Can 2. My mother _____in a middle school. A. teach B. teachs C. teaches 3. She doesn’t _____ her homework in theafternoon. A. todo B. does C. do 4. John usually _____ up at 6:30. · A. wake B. wakes C. waking
5. Eve _____ here every morning. A. come B. go 6. _____ she always come here A. Do B. Does C. Is 7. I _____ not know. A. am B. can C. do 8. ---_____ your sister usually have lunch at twelve ---Yes. A. Do C. / 】 9. Does she _____ morning exercises here every day A. does B. doing C. do 10. He _____ no time. A. have C. having 习题：选择 1.It’s time _____ lunch. Ａ．forＢ．toＣ．in 2.There is something wrong ______ his clock. Ａ．toＢ．withＣ．at 3.John usually _____ up at 6:20. ? Ａ．wakeＢ．wakesＣ．waking 4.But today he has _____ time. Ａ．noＢ．notＣ．isn’t
The way的用法及其含义（二） 二、the way在句中的语法作用 the way在句中可以作主语、宾语或表语： 1.作主语 The way you are doing it is completely crazy.你这个干法简直发疯。 The way she puts on that accent really irritates me. 她故意操那种口音的样子实在令我恼火。The way she behaved towards him was utterly ruthless. 她对待他真是无情至极。 Words are important, but the way a person stands, folds his or her arms or moves his or her hands can also give us information about his or her feelings. 言语固然重要,但人的站姿,抱臂的方式和手势也回告诉我们他(她)的情感。 2.作宾语 I hate the way she stared at me.我讨厌她盯我看的样子。 We like the way that her hair hangs down.我们喜欢她的头发笔直地垂下来。 You could tell she was foreign by the way she was dressed. 从她的穿著就可以看出她是外国人。 She could not hide her amusement at the way he was dancing. 她见他跳舞的姿势，忍俊不禁。 3.作表语 This is the way the accident happened.这就是事故如何发生的。 Believe it or not, that's the way it is. 信不信由你, 反正事情就是这样。 That's the way I look at it, too. 我也是这么想。 That was the way minority nationalities were treated in old China. 那就是少数民族在旧中
语法强化与扩展： 指示代词：this, that, these, those 1. this和these指说话人较近的人或物，that和those指说话人较远的人或物. this和that指单数，be动词用单数形式is,同时后面的名词用单数形式。these和those表示复数，be 动词用复数形式are,同时后面的名词用复数形式。 2. 在回答主语this或that的一般疑问句或特殊疑问句时，在答语中用it代替句中this 或that; What i s t hi s/that这是/那是什么It' s a/an...它是???： Is this/that...这是/那是???吗Yes, it is.是的，它是。No, it isn' t?不，它不是。 3. 在回答主语these或those的一般疑问句或特殊疑问句时，在答语中用they代替句中these 或those; What are these/those它们是什么They are...它们是???； Are these/those...这些/那些是?吗Yes, they are.是的，它们是。No, they aren* t. 不，它们不是。4. 在介绍某人时，用this或that,而不用he或she:例如This is my mum. 5. 打电话时，说自己是谄用This is...，问别人是谄用Who* s that )7. --------- 1s that Mary* s school bag 一：填空 1. I like pan ts. pan ts are red.（这些） 2. I don' t Ii ke shoes?shoes are too sma I I ?(那些) 3. I v/ant （这个）sweater. I don t want 个 sweater. （那个）is too big. ） 二：选择 ( )1. pen i s red?oenci I i s green? A. this, that B. These, Those C. That, Those D?Thi s, That ( )2. I s a panda over there A. this B. that C ■those D. these ( )3. two girls are Mary and Linda? A. This B. They C ■That D. Those ( )4. Look, what is It' s an eraser? A. this ( )5. Are your watches over there A. this ( )6. those his dietionaries A. Yes, it isn S?isn' t.
科普版小学四年级英语下册知识重点解析 1.Are you in Grade Four! 1.We are new. 我们是新生。 2.表达“几年级几班”，则需译为“Class×，Grade×”，英文表达方式与中文相反，英文需先说小单位，再说这个小单位所属的大单位，即由小到大，不能颠倒。如： 三年级（3）班 Class 3, Grade 3. 问某人在哪个年级，哪个班级时，用疑问句“What grade, what class”提问。 3.This way, please.请往这边走。 4. glass的用法 1) glass作为"眼镜"讲，应用复数形式，如：The old teacher has two pairs of big glasses. 在英语中手套gloves裤子pants，剪刀scissors均用复数形式。 2）glass作"玻璃杯"讲时则可用单数形式或复数形式，如： I want a glass of tea. I want two glasses of milk. 3) 而作为物质名词"玻璃"讲则要用作不可数名词，如： The boy broke two panes of glass. 5. Look! They are on your nose. 看！它（眼镜）就在你的鼻梁上。 英语中表达“戴着眼镜”，可以说“wear glasses”, 也可以说“ The glasses are on sb’s nose. Lesson 1 你是在四年级吗？ 说一说 比尔，吉尔：打扰一下！ 露露：什么事？ 比尔，吉尔：我们是新生。我们找不到自己的班级。 露露：你们是四年级的吗？ 比尔，吉尔：是，我们是的。 露露：你们在哪个班？ 比尔，吉尔：我们在三班。 露露：三班？请走这边。 趣味阅读奶奶的眼镜 我找不到我的眼镜了，它在哪呢？ 奶奶找不到她的眼镜了。 伊芙：在盒子里吗？ 奶奶：没有，不在盒子里。
六年级上册知识点 Lesson1&Lesson2 I. 频度副词 (1) 频度副词表示“次数多少” (2) 常见的频度副词有： always(100%的频度)，表“总是，常常”，侧重时间的连续性；usually(80%--90%的频度),表“通常”，强调习惯性，经常如此；often(50%--70%的频度)，表“经常，”指有规律的经常出现‘sometimes(30%--50%的频度)，表“有时候”，指偶尔出现；never(0%的频度)，表“从来不”，表示一种习惯。 习题：选择 1. His father always _____ him to school at 8:00. A. takes B. to take C. take 2.Sometimes Amy _____ TV in the evening. A. watch B. watching C. watching 3.He never _____ the floor. A. mop B. mopping C. mops 4.She always _____ breakfast at 7:00. A. make B. makes C. making 5.Does she always _____ sports at 9:00. A. does B. do C.doing II. 一般现在时 （1） 一般现在时通常表示疆场发生的动作或存在的状 态。 （2） a. be动词的一般现在时 人 肯定式否定式疑问式简略回答称，
数形式 第一人称单数I am a teacher. I am not a teacher. Am I a teacher? Yes, you are. No, you aren’t. 第二人称单数You are a teacher. You aren’t a teacher. Are you a teacher? Yes, I am. No, I’ not. 第三人称单数He/She is a teacher. He/She is not a teacher. Is he/she a teacher? Yes, he/she is. No, he/she isn’t. It is Mary.It isn’t Mary. Is it Mary?Yes, it is . No, it isn’t. 各人称复数We/You/They are teachers. We/You/They are not teachers. Are we/you/they teachers? Yes, you/we/they are. No, you/we/they aren’t. b.示意动词的一般现在时 人 称， 肯定式否定式疑问式简略回答
定冠词the的用法： 定冠词the与指示代词this ,that同源,有“那(这)个”的意思,但较弱,可以和一个名词连用,来表示某个或某些特定的人或东西. (1)特指双方都明白的人或物 Take the medicine.把药吃了. (2)上文提到过的人或事 He bought a house.他买了幢房子. I've been to the house.我去过那幢房子. (3)指世界上独一无二的事物 the sun ,the sky ,the moon, the earth (4)单数名词连用表示一类事物 the dollar 美元 the fox 狐狸 或与形容词或分词连用,表示一类人 the rich 富人 the living 生者 (5)用在序数词和形容词最高级,及形容词等前面 Where do you live?你住在哪? I live on the second floor.我住在二楼. That's the very thing I've been looking for.那正是我要找的东西. (6)与复数名词连用,指整个群体 They are the teachers of this school.(指全体教师) They are teachers of this school.(指部分教师) (7)表示所有,相当于物主代词,用在表示身体部位的名词前 She caught me by the arm.她抓住了我的手臂. (8)用在某些有普通名词构成的国家名称,机关团体,阶级等专有名词前 the People's Republic of China 中华人民共和国 the United States 美国 (9)用在表示乐器的名词前 She plays the piano.她会弹钢琴. (10)用在姓氏的复数名词之前,表示一家人 the Greens 格林一家人(或格林夫妇) (11)用在惯用语中 in the day, in the morning... the day before yesterday, the next morning... in the sky... in the dark... in the end... on the whole, by the way...
this, these, that, those 的用法 我们把this, these, that, those 这四个词称为“指示代词”，用来指示或标识人或事物。其中，this 和that 为单数指示代词，these 和those 为复数指示代词。例如： ?This is my mother. 这是我的妈妈。 ?That's my dad. 那是我的爸爸。 ?These are my parents. 这是我的父母。 ?Those are Paul's son and daughter. 那是保罗的儿子和女儿。 通常，我们谈论离自己近的人或物时用 this / these，离自己远的人或物时用that / those 。例如： ?I like these books, but I don't like those books. 我喜欢这些书，但是我不喜欢那些书。 ?This girl is Mary. 这个女孩是玛丽。 ?That boy is in Class 5. 那个男孩在五班。 下面我们来看一下这些指示代词作主语构成一般疑问句时，答句所使用的主语会有什么变化。 ?Is this your bike? ?Yes, it is ?. 这是你的自行车吗？ ?是的，是我的自行车。 ?Are these your grandparents? ?Yes, they are.
?这是你的祖父母吗？ ?是的，他们是。 由此可以看出，当指示代词所指的事物已确定时，后面的指示代词指人时用he、she 和they 来代替，指物时用it 和they 来代替。再如： ?Is that a bird or a plane? ?It's a plane. ?那是鸟还是飞机？ ?是飞机。 ?Is this your friend Tony ?Yes, he is. ?这是你的朋友托尼吗？ ?是的，他是。 上一个：Module1 动词be 说明身份、年龄、状态等 下一个：Module 3 there be 句型的用法
小学四年级下册英语测试卷 听力部分 一、听字母组合，选择正确的选项。 ( )1. A. pn B. en C.he ( )2. A. lg B.nj C.wo ( )3. A. S V B.U X C.T I ( )4. A. C N B.UZ C.LV ( )5. A. bd B.kd C. rf ( )6 A.MVN B.MYX C. NXT .二、听音，写数字。 1. ________ 2. ________ 3. ________ 4. ________ 5. _________ 三、听音，选出你所听到单词，并将其标号填入提前的括号内。( )1. A.bend B.friend C.head ( )2. A. leg B.red https://www.doczj.com/doc/eb4837664.html, ( )3. A. skip B.swim C. fish ( )4. A. hill B.let C. little ( )5. A. hand B. read C. run ( )6. A.what B. whose C. where ( )7. A.brother B. sister C. mother ( 8. A.apple B.banana C. orange ( )9. A.seven B. eight C. time 四、听音，请根据你所听到的句子，将其标号写在题前的括号内。 （）1. A. I can see thirteen. B. I see fourteen. C. I can see fifteen. D.I can see sixteen. （）2. A. She is from England. B. We are from England. C. He is from England. D. She isn’t from England. （）3. A. I am in Class Five. B. We’re in Grade Four. C. I am in. Grade Six. D. We’re in Class Four. （）4. A. Are they blue? B. They are brown.. C. They are black. D. They are yellow. （）5. A. They are my friends. B. She is my sister. C. He is my teacher. D. He is my brother. （）6. A. Welcome to our school. B. Welcome to our home. C. Welcome to Beijing. D. Welcome to China （）7. A. Is your mother a teacher? B. Is your mother a nurse? C. Is your mother a worker? D. Is your mother a doctor? （）8. A. These are monkeys. B. These are panadas. C. These are birds. D. These are rabbits.
“tｈｅwａｙ+从句”结构的意义及用法 首先让我们来看下面这个句子: Ｒead the foｌloｗｉnｇpassagｅａnd talkａbout ｉt wi ｔh your classmaｔes．Try tｏｔeｌl whaｔyｏu thiｎk ｏf Tom aｎd ｏｆｔhe ｗay the chiｌｄrenｔrｅated ｈim. 在这个句子中，ｔhe waｙ是先行词,后面是省略了关系副词that或in whｉch的定语从句。 下面我们将叙述“the ｗaｙ+从句”结构的用法。 1.tｈe wａy之后，引导定语从句的关系词是tｈat而不是hoｗ,因此，<<现代英语惯用法词典＞＞中所给出的下面两个句子是错误的：Ｔhｉs is ｔｈeｗayｈowｉtｈａppened. This is the way how he ａlwａｙs treats me. 2．在正式语体中,thaｔ可被in which所代替;在非正式语体中，ｔhat则往往省略。由此我们得到theｗay后接定语从句时的三种模式：1) tｈe ｗaｙ＋ｔhａt-从句２）the way +ｉn whiｃh－从句3) the ｗay +从句 例如：Ｔｈe way(in whiｃh ，thａt) ｔhｅｓｅｃomｒade ｓloｏｋａｔｐrobｌems is wrong．这些同志看问题的方法
不对。 Ｔｈｅｗａy(that ,ｉn ｗhiｃh)yoｕ’ｒe doinｇit is comple ｔeｌy crａzy.你这么个干法,简直发疯。 Wｅａdmiｒｅd him for thｅｗay ｉｎｗhｉch he fａｃeｓdiｆficultieｓ． Waｌlａｃe ａｎd Ｄarwiｎｇreed ｏn the way ｉｎwhi ｃh ｄｉfｆｅrｅnt forms ｏf life had ｂegｕn.华莱士和达尔文对不同类型的生物是如何起源的持相同的观点。 Thｉs is ｔｈe ｗaｙ（tｈａｔ) hｅdｉd it. I lｉkeｄｔhe waｙ(ｔhat) ｓｈeｏｒganized ｔhe ｍeetｉng． 3.theｗay(tｈat)有时可以与hｏw(作“如何”解）通用。例如： That’s tｈe ｗaｙ(tｈaｔ) shｅspoke. = Tｈat’s how shｅspoke.
指示代词this,that.these.those 注意 is/are的使用： this/that+可数名词单数或不可数名词+ is these/those＋可数名词复数（不可以加不可数名词）+are 例：离你较近的时候：this duck这个鸭子these ducks这些鸭子 离你较远的时候(经常与over there连用)：that duck 那个鸭子those ducks那些鸭子 常见句型： 1.What is this/that?这是/那是什么？ It’s a/an...它是... 2.Is this/that...?这是/那是...吗？ Yes,it is.是的，它是。No,it isn’t.不，它不是。 3.What are these/those?它们是什么？ They are...它们是... 4.Are these/those...?这些/那些是...吗？ Yes,they are.是的，它们是。No,they aren’t.不，它们不是。 【补充部分：名词规则变化】 1、一般情况（包括以e结尾的名词）,加-s 例：cup(杯子)-cups, cat-cats, cake－cakes, flag(旗子)-flags, face(脸)－faces 2、以s,x,ch,sh结尾,加-es 例：class(班级)-classes, box(盒子)-boxes, watch(手表)-watches, brush(刷子)-brushes 3、以辅音+y结尾变y为ies 例：city(城市)-cities, country(国家)-countries, study(书房)-studies 注意：以元音+y结尾,加-s boy-boys, ray(光线)-rays, day-days 4、以o 结尾 有生命加-es 例：mango(芒果)-mangoes, hero(英雄)-heroes, tomato(西红柿)-tomatoes, potato(土豆)-potatoes 没生命加-s 例：zoo(动物园)-zoos, photo(照片)-photos, piano(钢琴)-pianos 5、以f,fe结尾变f,fe为ves 例：leaf(叶子)-leaves, knife(小刀)-knives, wife(妻子)-wives
四年级英语教学计划 一、基本情况 四年级的小学生聪明活泼、勤奋好学，他们已经在三年级的时候初步接触了英语，所以对英语有着浓厚的兴趣。 二、教材分析 《九年义务教育小学英语用书》供三年级起使用，它根据小学生的心理和生理特点以及他、发展要求，培养他们学习英语的积极态度，使他们建立初步的学习英语的自信心。本册供以小学四年级为起点、开设英语的学校第一学年第二学期使用。 《九年义务教育小学英语用书》的设计和编写体现了外语教学思想的继承和发展。在分析、研究许多种国内外小学英语教材的基础上，取其精华，博采众长，形成了本套教材特有的编写体系。同时，有吸收了当今国内外英语作为外语教学的理论和成功经验，把这些教学理论和实践经验同我国的小学外语教学实际相结合，以形成我国小学英语的外语教学模式和教学方法。 本册教材具有以下几个特点： 1、注重学生语言运用能力的培养，突出语言的实践性和交际性，同时也突出语言的真实性和实用性。 2、注重学生自学能力和学习策略的培养，为学生的进一步学习或终身学习奠定基础。 3、注重中外文化的双向交流，使学生通过学习，培养未来跨文化交际所需要的能力。 4、注重学生学习兴趣的培养，以不同方式最大限度的激发学生的学习动机。 5、注重融合学科内容，加强学科之间的整合和渗透，让学生通过英语学习来获得其他学科的知识。 6、注重教材的灵活性和可操作性，以满足不同层次的学生的需求。 7、注重教学资料的配套，为学生提供良好的英语学习环境，帮助学生拓展自我发展的空间。 8、注重中小学各阶段的衔接，以保证各学段的顺利过渡，全面提高中小学英语教学的整体质量。 三、方法措施 1、认真备课，钻研教材，抓紧课堂教学，做到当堂内容当堂掌握。 2、运用各种不同的肢体语言来辅助教学。 3、在课堂上多开展一些有趣的活动、游戏让学生在活动中学习英语，在生活中学习英语。 4、多为学生营造一些学习氛围，如：创设英语角等等。 5、要求学生在课余时间尽量的运用已经学习的英语进行对话。 6、多看英语画报，多读英语故事，多看英语书籍。 7、多与学生交流，进行口语交际训练。 四、教学内容与课时安排 Lesson1 Are you in Grade Four 3课时
表示“方式”、“方法”，注意以下用法： 1.表示用某种方法或按某种方式，通常用介词in(此介词有时可省略)。如： Do it (in) your own way. 按你自己的方法做吧。 Please do not talk (in) that way. 请不要那样说。 2.表示做某事的方式或方法，其后可接不定式或of doing sth。 如： It’s the best way of studying [to study] English. 这是学习英语的最好方法。 There are different ways to do [of doing] it. 做这事有不同的办法。 3.其后通常可直接跟一个定语从句(不用任何引导词)，也可跟由that 或in which 引导的定语从句，但是其后的从句不能由how 来引导。如： 我不喜欢他说话的态度。 正：I don’t like the way he spoke. 正：I don’t like the way that he spoke. 正：I don’t like the way in which he spoke. 误：I don’t like the way how he spoke. 4.注意以下各句the way 的用法： That’s the way (=how) he spoke. 那就是他说话的方式。 Nobody else loves you the way(=as) I do. 没有人像我这样爱你。 The way (=According as) you are studying now, you won’tmake much progress. 根据你现在学习情况来看，你不会有多大的进步。 2007年陕西省高考英语中有这样一道单项填空题： ——I think he is taking an active part insocial work. ——I agree with you_____. A、in a way B、on the way C、by the way D、in the way 此题答案选A。要想弄清为什么选A，而不选其他几项，则要弄清选项中含way的四个短语的不同意义和用法，下面我们就对此作一归纳和小结。 一、in a way的用法 表示：在一定程度上，从某方面说。如： In a way he was right.在某种程度上他是对的。注：in a way也可说成in one way。 二、on the way的用法 1、表示：即将来(去)，就要来(去)。如： Spring is on the way.春天快到了。 I'd better be on my way soon.我最好还是快点儿走。 Radio forecasts said a sixth-grade wind was on the way.无线电预报说将有六级大风。 2、表示：在路上，在行进中。如： He stopped for breakfast on the way.他中途停下吃早点。 We had some good laughs on the way.我们在路上好好笑了一阵子。 3、表示：(婴儿)尚未出生。如： She has two children with another one on the way.她有两个孩子，现在还怀着一个。 She's got five children，and another one is on the way.她已经有5个孩子了，另一个又快生了。 三、by the way的用法
科普版英语四年级下册教案(全册)
课题: Lesson 1 Are you in Grade Four ? 教学内容: 1.Let’s talk . 教学目标: 1.能听懂.会说.会认读way, they, behind, new, table.并能根据中文 拼写出英文. 2.能听懂.会说交际用语,并能用来进行对话. 教学重难点: 1.词汇. 2.交际用语. 教学方法: 自问自答法. 教具准备: 录音机. 教学过程: 一. 学习单词: 教师把本课要求掌握的8个生词写在黑板上,教师领读几遍,让学生自己读,直到熟练为止. 二.学习Let’s talk : 2
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A: We are ( ).We can’t find our ( ). B: Are you in ( ) Four ? A: Yes , we ( ). B: What class are you ( ) A: We’re in ( ) Three . B: Class Three ? This ( ) , please . 教学内容: 1. Let’s learn . 2. Let’s sing . 3．Read for fun . 4. Listen and tick . 教学目标: 1．掌握主题句型. A: Are they in Grade Four ? Yes , they are ./No ,they aren’t . B: What grade are they in ? They are in Grade Four . 2、会唱歌曲. 教学重点: 4
能理解和掌握主语为复数的主系表结构,并能用替换词造句. 教学方法: 简笔画情景教学法. 教具准备: 简笔画. 教学过程: 一. 复习检查: 1.复习生词:复习上课时所学的8个生词,其中要求四会的五个词可由教师说中文,让学生写出英文,其余三个只要求三会的词,可由教师说英文,让学生写出中文. 2.本课对话:先放一遍录音,然后按上一课时布置的分组,叫若干组学生站起来表演对话. 二. 导入新课: 1.复习和学习生词. 先复习已学过的单词class , grade ,classroom 等,教师可说中文”三班”.”五年级”. 等,让学生说英文,再从<<活动资料>>中取出reading room 和classroom 等的简笔画,边画边读单词.然后由教师说reading room 等,让学生举图,再由教师举图,由学生英文. 5
2015六年级英语上册重点知识（新版科普 版） 六年级英语上册重点句型 Unit1Areyougoingtohaveabirthdayparty? 1.重点词汇 weather天气（可数或者不可数） sunny晴朗的（名词变形容词） will将要（情态动词+动词原形） begin开始（begintodosth.） 2.重点短语 aeacae做蛋糕 invitesoefriends邀请朋友 singanddance唱歌跳舞 eatnoodles吃面条 visityfriends拜访朋友 taeswiinglessons上游泳课 dosoewashing洗刷 bytheway顺便问一下 3.重点句型（考试必备） ybirthdayiscoing. Areyougoingtoaeacae?yes,Ia./No,Ianot. I’goingtohaveapartyathoenextSundayevening.
Wouldyoulietocoe? ThisisyplanforthisSunday. Whataboutyourplan? onay3rd,I’goingtohelpyudosoewashing. Theweatherisgood. Thepartywillbeginatfouro’cloc. I’asingyuncleandaunttocoetoyparty. couldIbringhitotheparty? 4.必考语法 一般将来时 时：toorrow、thedayaftertoorrow,next+时间，in+将来的时间等 态：主语+will+动词原形+其他. 主语+shall+动词原形+其他.（适合主语时第一人称）主语+begoingto+动词原形+其他. 句型： 否定句：主语+will+not+动词原形+其他. 主语+shall+not+动词原形+其他.（适合主语时第一人称） 主语+begoingto+not+动词原形+其他. 疑问句： 一般疑问句；will/shall+主语+动词原形+其他？
科普版英语四年级下册教案(全册) 教学内容: 1.Let’s talk . 教学目标: 1.能听懂.会说.会认读way, they, behind, new, table.并能根据中文拼写出英文. 2.能听懂.会说交际用语,并能用来进行对话. 教学重难点: 1.词汇. 2.交际用语. 教学方法: 自问自答法. 教具准备: 录音机. 教学过程: 一. 学习单词: 教师把本课要求掌握的8个生词写在黑板上,教师领读几遍,让学生自己读,直到熟练为止. 二.学习 Let’s talk : 本课的对话可以用自问自答导入法导入,教师可同时充当Jill, Bill和Lulu 三个角色,先站在右边充当Jill 和Bill ,说”Excuse me , .please.”再转到左边充当Lulu ,说” Yes ?” ,再转回右边充当Jill和Bill 说” We are new . We can’t find our classroom.”一直到将全段对话表演完,表演两遍后放录音,先将全段放一遍,然后逐句放,让学生逐句跟说并翻译成中文. 三. 操练: 将对话分成三段, 各配一幅简笔画,教师写出关键词,然后逐段操练.操练的顺序是:先让学生听录音并跟说两遍,再让他们连起来说,并给他们半分钟时间让他们根据关键词复述,然后让全班复述. 在三段都操练完毕后,让同座间充当不同角色进行对话,一人充当Bill,另一人充当Lulu, 三段连起来练习,最后叫若干对同学站起来复述全段对话,然后将学生按三人一组分组,要求他们在下一堂课上进行表演. 四.作业:
让学生课下练习,准备下节课进行表演. 五. 效果测试: 根据Let’s talk.的内容填空 A: Excuse ( ) , please. B: Yes ? A: We are ( ).We can’t find our ( ). B: Are you in ( ) Four ? A: Yes , we ( ). B: What class are you ( ) A: We’re in ( ) Three . B: Class Three ? This ( ) , please . 教学内容: 1. Let’s learn . 2. Let’s sing . 3．Read for fun . 4. Listen and tick . 教学目标: 1．掌握主题句型. A: Are they in Grade Four ? Yes , they are ./No ,they aren’t . B: What grade are they in ? They are in Grade Four . 2.会唱歌曲. 教学重点: 能理解和掌握主语为复数的主系表结构,并能用替换词造句. 教学方法: 简笔画情景教学法. 教具准备: 简笔画. 教学过程: 一. 复习检查: