![](https://webarchive.library.unt.edu/web/20201219150622im_/https://www.ncbi.nlm.nih.gov/Structure/IMG/spacer.gif)
text terms (key words): A wide variety of text terms, such as names of biosystems, genes, proteins, and small molecules can be used to search the BioSystems database. You can also search for other words that might be present in the title, comments, or other text containing fields of a record. Because terminology can vary across records, it can be helpful to include synonyms in your query (e.g., PTGS1 OR "prostaglandin endoperoxide synthase 1"). It is also possible to search for a word stem by using an asterisk (*) as a wild card; for example, arachidon* will retrieve records with terms such as arachidonate, arachidonic, arachidonoyl. The Entrez Help document provides additional information about truncating search terms in this way.
unique identifiers: BioSystem records can be retrieved by searching for the unique identifiers of their components, such as GeneIDs, protein sequence GI numbers or accession numbers, and CIDs, SIDs, or external registry names of small molecules. The retrieved biosystems have been associated with those components through the methods descibed in the data processing/create direct links section of this document.
organism: To retrieve biosystem records for a specific organism or organism group, you can enter its common name (e.g., human) or scientific name (e.g., Homo sapiens), or other taxonomic node (e.g, Primates) in the Organism [orgn] search field. Note that a search of the organism field will retrieve only organism specific biosystems that fall under the specified taxonomic node. To find corresponding conserved biosystems that are present in numerous organisms, simply follow the "related biosystems/conserved biosystems" link from the biosystem record(s) of interest.
database subset: It is possible to retrieve records from a specified database subset. For example, the SourceName search field allows you to retrieve records from a specific source database. The Filter field allows you to limit a search to specific record types or to records that have links to another Entrez database of interest; for example, a search for biosystems_structure[filter] will retrieve biosystem records that have links to the Entrez Structure database, and a search for biosystems_omim[filter] will retrieve biosystem records that have links to the Online Mendelian Inheritance in Man (OMIM) database.
and more... The biosystems database can also be searched by terms that appear in any of the other search fields.
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A variety of techniques can be used to search the database, offering varying degrees of control over your query. In some cases, they offer alternative ways of executing the same search (as is true for sample searches #4, #5, and #6 below), with each method offering different benefits. The search methods include:
Method |
Description |
Example |
Basic Search |
Just enter search terms without specifying search fields, other limits, or Boolean operators.
The "Search Details" box in the right margin of the search results page shows exactly how Entrez parsed and handled your query. If desired, you can edit the query in that box and press the "Search" button to run the modified query.
The "See more..." link a the bottom of the "Search Details" box opens a more detailed display:
- The Query Translation box shows the search strategy used to run the search
- To edit the search in the Query Translation box, add or delete terms and then click Search.
- Click URL to display the current search as a URL to bookmark for future use. Searches created using History numbers can not be saved using the URL feature.
- You may also save your search using My NCBI.
- The Result number link retrieves the documents found and displays them in a search results page.
- Translations details how each term was translated using Entrez's search rules and syntax for the database.
- User Query shows the search terms as you entered them in the search box and any syntax errors with the query.
|
Search #1:
human arachidonic acid
will retrieve biosystems with those terms anywhere in the record.
Some of the records might be from organisms other than human because we did not limit that search term to the Organism search field. Therefore, we will also retrieve other species biosystems if they happen to contain the term "human" in a comment or some other field of the record.
Similarly, the term "arachidonic acid" can appear anywhere in the record. Some biosystems might have it in the title, and others might have it as a biosystem component.
The terms entered in a basic search may or may not be adjacent to each other in the retrieved records, depending on how Entrez parsed the query (as shown in the Search Details for a given search). To force terms to be searched as a phrase, use quotes. To refine your search in other ways, use the Limits option or the Advanced Search methods described below. |
Limits |
The Limits page allows you to restrict your search in various ways.
At a minimum, the Limits page displays the list of available search fields. You can do a separate search for each term or phrase in your query, as shown in sample Search #2 and #3 to the right, and select the desired search field for each one. (If desired, you can then combine the searches by using the Search Builder or History section of the Advanced Search page.)
For some databases, the Limits page also provides other commonly used options, as check boxes and/or pull-down menus, for restricting your search results to records with specific characteristics. These check boxes and pull-down menus generally represent a commonly used subset of the choices that are available from the Advanced Search page and are placed on the Limits page for easy access.
IMPORTANT NOTE: Once you have used a particular Limit, warning sign will appear near the top of your search results page that indicates which Limit(s) are currently in effect, for example:
![image of the Limits folder that displays a deactivated check box, showing that the limits you most recently selected for a search are no longer in effect](https://webarchive.library.unt.edu/web/20201219150622im_/https://www.ncbi.nlm.nih.gov/Structure/IMG/entrez/entrez3_warning_limits_activated.png)
Note that the Limit will remain in effect for all subsequent searches in the current database unless you change or remove that limit. In the illustrated example above, any search you do will be limited to the Titles of records, until you remove the limit.
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Search #2:
On the BioSystems search page, click on the Limits link, select the Organism search field, and enter the following query:
human
and press "GO". That will retrieve only biosystems found in human.
Search #3:
Open the Limits page again and clear your previous search. Change the search field selection to Title, enter the following query:
arachidonic acid
and press "GO". That will retrieve only records containing those terms in the title, or name, of a biosystem.
If desired, you can then combine the searches on the Advanced Search page, either by using the Search Builder, as shown in sample Search #4, or by using the History section of that page, as shown in sample Search #5.
|
Advanced Search |
The Advanced Search page allows you to exercise greater control over your search, for example, by enabling you to:
- Build a search one step at a time.
- Browse the index of any search field and add term(s) of interest from the index to the active query box at the top of the page.
- View your search History and combine or subtract searches from each other.
As you build a query, either by using the Search Builder's pull-down menus, or by using the "Add" links in the "History" portion of the page to combine previous searches, the grey text box at the top of the page will display your current query.
You can also manually edit the current query by clicking the "Edit" link beneath the grey text box. That will allow you to type terms/search numbers/etc. directly into the box, add parentheses for nesting if desired, change Boolean operators, etc.
In addition, the following types of advanced searches can be entered in the query box of any Entrez search page (i.e., in the query box of the database's Home page, Limits page, or Advanced Search page):
(A companion tool, FLink, is available for Batch queries.)
|
Search Builder |
The "Search Builder" section of the Advanced Search page allows you to build your query step by step, adding a new search term and selecting a new search field at each step. It also allows you to browse the index of any search field to view the available terms.
To build a query:
(1) Select the Search Field of interest using the pull-down menu.
(2) Type a term(s) in the text box beside the search field menu. Or, use the "Show index list" link to see the index of the search field and select the desired term from the index. (tips on using the "Show Index List")
(3) Select the Boolean operator (AND, NOT, OR) that should precede the term when it is added to the active query at the top of the page.
Continue the above steps, as desired, to add more term/search field combinations to your query.
As you use the Search Builder, the grey text box at the top of the page will show your current query.
You can manually edit the current query by clicking the "Edit" link beneath the grey text box. That will allow you to type terms/search numbers/etc. directly into the box, add parentheses for nesting if desired, change Boolean operators, etc.
Press the Search button to display the records retrieved by your search (i.e., it displays the search results page).
Click on the "Add to history" link if you prefer to simply add the query to your search history and remain on the Advanced Search page, where you can continue building your query.
Tips on using the "Show Index List" function on the Advanced Search page:
The "Show Index List" function allows you to browse the index of any Search Field. If you select a search field and press the "Show Index" link without entering a term in the box, you will be taken to the top of the index. If you enter a term first, you will be taken to the part of the index that contains your term (or the closest alphabetical location, if your term is not present in the index).
The number of records that contain the term will appear in parentheses. You can also browse the index to explore the variety of terms available (for example, select "All Fields", enter "Huntington", and click on the "Show Index" link to see additional spellings and/or related terms, such as Huntington disease, Huntington's, Huntington's disease).
![illustration showing how the Index button can be used to view the list of terms that are available in the selected search field](https://webarchive.library.unt.edu/web/20201219150622im_/https://www.ncbi.nlm.nih.gov/Structure/IMG/entrez/entrez_index_button_Entrez3.png)
To select a range of terms from the index, use the Shift key while selecting the first and last term. Then use the AND, OR, or NOT buttons to add that group of terms to the active query.
To select multiple terms that do not fall within a continuous range from the index, use the Control key while selecting the terms of interest. Then use the AND, OR, or NOT buttons to add that group of terms to the active query.
Note: When multiple terms are selected from the index window, they are OR'ed together within parentheses and then appended to your query with whatever Boolean operator you have selected.
|
Search #4:
On the BioSystems search page, click on Advanced Search and build your search one step at a time:
(a) Using the first pull-down menu in Search Builder, select the Organism search field and enter the following query:
human
and select "AND" as the Boolean operator. That term/search field selection will automatically be displayed in the grey text box at the top of the page, which shows your current query.
(b) Using the second pull-down menu in Search Builder, select the Title search field and enter the following query:
arachidonic acid
and select "AND" as the Boolean operator. That newest term/search field selection will automatically be added to the grey text box at the top of the page
(c) your query will now appear as:
human[Organism] AND arachidonic acid[Title]
Press the Search button if you want to display the records retrieved by your search (i.e., it displays the search results page).
Or, click on the "Add to history" link if you prefer to just add the query to your search history and remain on the Advanced Search page, where you can continue building your query.
Note that this search will produce the same results as sample searches #5 and #6. It is simply executed in a different way. That is, you remain on a single query page (Advanced search) and can browse the index of any search field as you build your query one step at a time.
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History |
The "History" section of the Advanced Search page displays the searches you have done in the current database.
You can combine or subtract searches from each other by entering the search numbers and the AND, OR, or NOT Boolean operators in the query box, for example: #2 AND #3. If the query contains several search numbers and Boolean operators, the Boolean operators are processed from left to right unless parentheses are used for nesting. If parentheses are used, the portions of the query in parentheses will be processed first, then the remaining Boolean operators will be processed from left to right.
Additional details about Search History:
- The Search History will be lost after 8 hours of inactivity. (To save a search indefinitely, click on the search # and select "Save in My NCBI.")
- Click "Clear History" to delete all searches from History.
- Entrez will move a search statement number to the top of the History if a new search is the same as a previous search.
- History search numbers may not be continuous because some numbers are assigned to intermediate processes, such as displaying a citation in another format.
- The maximum number of searches held in History is 100. Once the maximum number is reached, PubMed will remove the oldest search from the History to add the most current search.
- A separate Search History will be kept for each database, although the search statement numbers will be assigned sequentially for all databases.
- PubMed uses cookies to keep a history of your searches. For you to use this feature, your Web browser must be set to accept cookies.
- Database records that you have copied to the Clipboard are represented by the search number #0, which may be used in Boolean search statements. For example, to limit the records you have collected in the Clipboard to those from human, use the following search: #0 AND human[organism]. This does not change or replace the Clipboard contents.
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Search #5:
Use the search numbers shown in the "History section" of the advanced search page to combine previous searches (for example, searches #2 and #3 shown above).
To do that, you can either:
Click on the "Edit" link beneath the grey text box and type in a search statement such as:
#2 AND #3
Or, instead of typing the search statement, use the "Add" link beside any search number in the "History" section of the Advanced Search page to add that search number into the grey text box.
That will retrieve only records that contain "human" in the Organism field and "arachidonic acid" in the Title field. Compare the retrieval from this search with that of the sample basic search above.
(Note that your search numbers might be different from those shown here, if you did earlier searches in the Entrez system before trying these examples.)
|
Complex Boolean |
Whether you are on the Basic search page (i.e., the database's home page), the Limits page, or the Advanced search page, you can:
Enter a search in command language, specifying your exact combination of desired search terms, search fields, and Boolean operators, as shown in the examples to the right. The syntax is:
term[field] BOOLEAN term[field] BOOLEAN term[field] etc.
Search Field names must be placed in square brackets [], and can be written as either the full name, for example, [BioSystemType], or as the corresponding search field abbreviation, for example, [Type]. (additional examples)
Boolean operators (AND, OR, NOT) must be written in UPPER CASE.
Boolean operators are processed from left to right unless parentheses are used for nesting. If parentheses are used, the portions of the query in parentheses will be processed first, then the remaining Boolean operators will be processed from left to right.
Boolean operators can also be used to combine or subtract searches from each other (i.e., to find the union, difference, or intersection of the data sets retrieved by various searches). To do this, use the Search History section of the Advanced Search page and simply enter the search numbers and desired Boolean operators in the query box.
For example, to identify the records that were retrieved by Search #2 of your search history, and also by Search #3, you could enter the following query:
#2 AND #3
To identify the records that were retrieved by Search #2 but not by Search #3, you could enter the following query:
#2 NOT #3
|
Search #6:
Simply enter all search terms and search fields as a single statement into the query box:
human[Organism] AND arachidonic acid[Title]
Note that this search will produce the same results as sample searches #4 and #5, but it takes only a single step when entered directly into the search box as a Boolean query.
Search #7:
(PTGS1[GeneName] OR "prostaglandin endoperoxide synthase 1"[GeneName]) NOT (primates[Organism] OR rodents[Organism])
This search will retrieve biosystem records that contain PTGS1 or prostaglandin endoperoxide synthase 1 in the GeneName field, but that will not be from any organisms in the taxonomic orders Primata or Rodentia.
|
Range Search |
Range queries are constructed by specifying a lower and upper numerical value separated by a colon (:) to specify the range, followed by a search field name or abbreviation in square brackets, as shown in the examples to the right. You can insert a space on each side of the colon but that is not necessary; the search will work either way.
All "count" fields (such as CID count, SID count, Gene count, and Protein count) and all dates can be range queried.
Range queries on "counts" have the format:
FromCount : ToCount [fieldname]
Note: The FromCount and ToCount values are integers. An example is shown to the right, as Search #8. The search fields summary table includes the names and abbreviations for the various "counts" fields.
Range queries on Dates (such as CreateDate or ModifyDate) have a similar format:
FromDate : ToDate [fieldname]
Note: The FromDate and ToDate values can specify an exact date, a month, or a year, and are written in the format: YYYY/MM/DD, YYYY/MM, or YYYY. An example is shown to the right, as Search #9. The search fields summary table includes the names and abbreviations for the various "date" fields.
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Search #8:
8:15[GeneCount]
will retrieve biosystems that are linked to as few as 8 Gene IDs through as many as 15 Gene IDs.
Search #9:
2011/04/10[CDAT] : 2011/05/25[CDAT]
will retrieve records that have a CreateDate [CDAT] from April 10, 2011 through May 25, 2011 (i.e., it will retrieve records that were first imported into the NCBI BioSystems database between those dates).
|
Batch Query |
FLink is a tool that was developed to handle large quantities of input and output data. It enables you to traverse from a group of records in a source database to a ranked list of associated records in a destination database.
For example, it can accept up to 100,000 protein sequence, gene, or small molecule identifiers as input and retrieve a ranked list of up to 100,000 biosystems.
An illustrated quick start guide shows the easy 1-2-3 step process for using the tool. The help document also provides details about the proper formatting of the (1) input UID list, the features of the (2) review + select display and (3) output display.
Although FLink was initially developed as a companion tool for the BioSystems database, it can also be used in a similar way for other types of input and output data, as noted in the list of FLink's supported databases.
|
|
Additional details about search methods and options are provided in the: (1) PubMed help document (including information about temporarily saving records from your search results to the Clipboard); (2) My NCBI help document (including information about Saving search strategies and indefinitely saving records from your search results into your My NCBI Collections); and (3) general Entrez help document.
![](https://webarchive.library.unt.edu/web/20201219150622im_/https://www.ncbi.nlm.nih.gov/Structure/IMG/spacer.gif)
By default, Entrez searches All Fields of the database unless a specific search field is indicated in the query. Search fields can be selected from pop-up menus on either the Limits and Advanced Search page, or can be typed directly in your query (surrounding field names with square brackets [], for example, [Organism] or [Orgn]).* The Show Index link on the Advanced Search page allows you to browse the index of each search field, where you can see the available terms, the number of records containing each term or phrase, as well as the syntax for entering values in search fields such as CreateDate or ModifyDate.
The currently available fields include:
Field name |
Abbreviation* |
Description |
Sample Search |
All Fields |
[ALL] |
Searches the complete database record |
"arachidonic acid"[all]
will retrieve the Biosystems records that contain the phrase "arachidonic acid" in any field of the record.
(Compare these search results with those obtained by the sample Title field search, which will retrieve records containing that phrase only in the biosystem title.)
The quotes surrounding the search terms ensure they are searched as a phrase. |
Accession |
[ACCN] |
Searches only the accession number of the biosystem record, which is always an alphanumeric combination (e.g., bsid12345).
(If you enter only the digits from the accession (e.g., 12345), use the UID field instead) |
bsid82991[accn]
will retrieve the biosystem record that contains the specified unique identifier in the accession number field. |
BioSystemType |
[Type] |
Allows you to retrieve, or limit your search results to, a specific type of biosystem record. Currently available types include:
pathway |
A series of related biochemical reactions. Some source databases, such as KEGG and Reactome, organize pathways hierarchically into supersets and subsets (KEGG refers to its subsets as "pathway modules"). The BioSystems database includes both supersets and subsets and provides cross-references between them. This category of records in the NCBI BioSystems database also includes biological processes from Gene Ontology (GO).
![](https://webarchive.library.unt.edu/web/20201219150622im_/https://www.ncbi.nlm.nih.gov/Structure/IMG/spacer.gif) |
|
structural complex |
Biomolecules and/or chemicals that are bound to each other as asserted by the source database. This category of records in the NCBI BioSystems database also includes cellular components from Gene Ontology (GO). |
|
signature module |
A group of genes that have a pathogenicity or other phenotype associated with them. |
|
functional set |
A group of enzymes that perform a certain function, for example, all aminoacyl transferases. This category of records in the NCBI BioSystems database also includes molecular functions from Gene Ontology (GO). |
|
|
pathway[BioSystemType]
OR
pathway[Type]
will retrieve only pathways from the the BioSystems database.
Similarly:
structural complex[Type]
will retrieve all structural complex records from the NCBI BioSystems database, and
functional set[Type]
will retrieve all functional set records from the NCBI BioSystems database.
|
CID |
[CID] |
PubChem Compound identifiers (CIDs) found in a biosystem using the method descibed in the data processing/create direct links/small molecules section of this document. |
5280883[cid]
will retrieve biosystems that include prostaglandin G2 (PGG2, CID 5280883) as a component. |
CIDCount |
[CIDCount] |
Total number of PubChem Compound identifiers (CIDs) linked to a biosystem using the method descibed in the data processing section of this document.
Fields such as CID count, SID count, Gene count, and Protein count, taken individually or together, give an indication of the relative size of the biosystem record. For example, BioSystem records with large counts may be Superset biosystems, whereas records with small counts may be Subset biosystems. |
10:23[CIDCount]
will retrieve biosystems that are linked to as few as 10 PubChem CIDs through as many as 23 PubChem CIDs.
(more about range searching...) |
ChemicalName |
[CN] |
Names of small molecules that are components in a biosystem. The names include the first four synonyms listed in the PubChem compound records that have been associated with the biosystem through the method described in data processing/create direct links/small molecules. For example, the first four synonyms listed in PubChem CID 5280883 are prostaglandin G2, PGG2, CHEBI:27647, and LMFA03010009; a search for any one of these names will retrieve biosystems that include PGG2 as a component. |
PGG2[cn]
will retrieve biosystems that include PGG2 as a component. |
Comments |
[COM] |
Comments and additional information provided by the source database on the biosystem |
|
CreateDate |
[CDAT] [PDAT] [DP] |
The date the biosystem record first appeared in the NCBI biosystems database. This is sometimes referred to as the publication date, hence the synonymous abbreviations PDAT and DP. The syntax for searching the field is YYYY/MM/DD, YYYY/MM, or YYYY. The colon (:) can be used to search for a range of dates, for example, YYYY/MM/DD:YYYY/MM/DD[CDAT]. |
2011/04/10[CDAT] : 2011/05/25[CDAT]
will retrieve records that were first imported into the NCBI BioSystems database from April 10, 2011 through May 25, 2011.
(more about range searching...)
|
Description |
[DESC] |
The text description of a biosystem provided by the source database. |
|
Filter |
[FILT] |
The "Filter" search field allows you to narrow your retrieval to records that have certain attributes, such as record type (e.g., conserved biosystem or organism specific biosystem).
It also allows you to limit search results to biosystem records that have links to other Entrez databases of interest, as shown in the sample search to the right. A detailed explanation of each type of link is provided in the description of an Entrez search results page.
The Filter field can also be used to view current database statistics, by entering a search for All[Filt], as shown in the example in the next column. |
conserved biosystem[filt]
will retrieve only that record type from the BioSystems database.
biosystems_structure[filt]
will retrieve the BioSystems records that have associated data in the Entrez Structure database.
You can then open the "Display" menu near the top of the BioSystems search results page and select Structures to retrieve the corresponding Entrez Structure records (for all biosystems records you have retrieved, or only for those whose checkboxes have been activated). The 3D structure records can then be viewed interactively using the free Cn3D software program.
all[filt]
will retrieve all of the biosystem database records, showing the total number retrieved.
|
GeneCount |
[GeneCount] |
Total number of Entrez Gene IDs linked to a biosystem using the method descibed in the data processing section of this document.
Fields such as CID count, SID count, Gene count, and Protein count, taken individually or together, give an indication of the relative size of the biosystem record. For example, BioSystem records with large counts may be Superset biosystems, whereas records with small counts may be Subset biosystems. |
8:15[GeneCount]
will retrieve biosystems that are linked to as few as 8 Gene IDs through as many as 15 Gene IDs.
(more about range searching...) |
GeneExternalID |
[GEID] |
The identifier given to a gene by the source of a biosystem. |
|
GeneID |
[GID] |
NCBI Entrez Gene IDs found in a biosystem using the method descibed in the data processing/create direct links/genes section of this document. Entrez GeneIDs are numerical identifiers for a genetic locus that remain stable regardless of changes to the locus name, coordinates, or sequence data. |
5742[gid]
will retrieve biosystems that include the Entrez GeneID 5742 (human PTGS1 gene) as a component. |
GeneName |
[GN] |
Gene name, including all of the synonyms found in the corresponding Entrez Gene record. For example, prostaglandin-endoperoxide synthase 1 (GeneID 5742) has the following synonyms listed in its Entrez Gene record: COX1; COX3; PHS1; PCOX1; PGHS1; PTGHS; PGG/HS; PGHS-1; PTGS1. Any of these synonyms can be searched in the Gene Name field to retrieve biosystems that include the gene as a component. |
PTGS1[gn]
will retrieve biosystems that include the human PTGS1 gene (Entrez GeneID 5742) as a component. |
ModifyDate |
[MDAT] |
The date the biosystem record last changed in the NCBI biosystems database. The syntax for searching the field is YYYY/MM/DD, YYYY/MM, or YYYY. The colon (:) can be used to search for a range of dates, for example, YYYY/MM/DD:YYYY/MM/DD[MDAT]. |
2011/04/10[MDAT] : 2011/05/25[MDAT]
will retrieve biosystem records that were modified from April 10, 2011 through May 25, 2011.
(more about range searching...)
|
Organism |
[ORGN] |
Organism(s) in which a biosystem is found. A common name (e.g., human), scientific name (e.g., Homo sapiens), or other taxonomic node (e.g, Primates or Primata) can be entered as a query.
Note that a search of the organism field will retrieve only organism specific biosystems that fall under the specified taxonomic node. To find corresponding conserved biosystems that are present in numerous organisms, simply follow the "related biosystems/conserved biosystems" link from the biosystem record(s) of interest. |
human[orgn]
will retrieve biosystems found in human.
primates[orgn]
will retrieve biosystems found in individual species falling in the order Primata.
|
ProteinCount |
[ProteinCount] |
Total number of Entrez Protein IDs linked to a biosystem using the method descibed in the data processing section of this document.
Fields such as CID count, SID count, Gene count, and Protein count, taken individually or together, give an indication of the relative size of the biosystem record. For example, BioSystem records with large counts may be Superset biosystems, whereas records with small counts may be Subset biosystems. |
15:28[ProteinCount]
will retrieve biosystems that are linked to as few as 15 Protein IDs through as many as 28 Protein IDs.
(more about range searching...) |
ProteinID |
[PID] |
This field contains the GI numbers and accession numbers of proteins found in a biosystem using the method descibed in the data processing/create direct links/proteins section of this document. |
A search for either
AAA03630[pid]
OR
189887[pid]
will retrieve biosystems containing the protein sequence record that has accession number AAA03630 (GI number 189887).
|
ProteinName |
[PN] |
Names of proteins in a biosystem. The names are extracted from the definition line of protein sequence records that have been associated with the biosystem using the method descibed in the data processing/create direct links/proteins section of this document. |
"prostaglandin endoperoxide synthase 1"[pn]
will retrieve biosystems containing a protein component with that name.
The quotes surrounding the search terms ensure they are searched as a phrase. |
SID |
[SID] |
PubChem Substance identifiers (SIDs) found in a biosystem using the method descibed in the data processing/create direct links/small molecules section of this document. |
|
SIDCount |
[SIDCount] |
Total number of PubChem Substance IDs linked to a biosystem using the method descibed in the data processing section of this document.
Fields such as CID count, SID count, Gene count, and Protein count, taken individually or together, give an indication of the relative size of the biosystem record. For example, BioSystem records with large counts may be Superset biosystems, whereas records with small counts may be Subset biosystems. |
12:25[SIDCount]
will retrieve biosystems that are linked to as few as 12 Protein IDs through as many as 25 PubChem SIDs.
(more about range searching...) |
SidExternalID |
[SEID] |
External registry names for small molecules that are found in a biosystem record, using the method descibed in the data processing/create direct links/small molecules section of this document. |
|
SourceAccession |
[SACC] |
The accession number assigned to a biosystem by the source database.
For example, the NCBI BioSystem record bsid82991, for human arachidonic acid metabolism, is derived from KEGG record hsa00590. Hsa00590 is the source accession. |
hsa00590[sacc]
will retrieve the KEGG organism specific biosystem for human arachidonic acid metabolism.
ko00590[sacc]
will retrieve the KEGG conserved biosystem for arachidonic acid metabolism. |
SourceID |
[SRCID] [SRID] |
A numerical identifier that is assigned to a particular source database of biosystem records. |
1[srcid]
will retrieve records deposited by the BioCyc database.
2[srcid]
will retrieve records deposited by the KEGG database.
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SourceName |
[SRC] [SRCN] [SRNM] |
Name of the organization that is the source of the record. (See the source databases section of this document for details.)
You can also see the allowable values in the SourceName field by using the Show index link on the Advanced Search page. |
biocyc[src]
will retrieve records deposited by the BioCyc database.
kegg[src]
will retrieve records deposited by the KEGG database.
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Title |
[TI] [TITL] |
Contains the brief title (or name) of the biosystem, for example, "arachidonic acid metabolism", or "citrate cycle", or "TCA cycle", etc. as assigned by the source database. |
"arachidonic acid"[ti]
will retrieve records with that phrase in the biosystem title.
(Compare these search results with those obtained by the sample All Fields search, which will retrieve biosystem records containing that phrase anywhere in the record.)
The quotes surrounding the search terms ensure they are searched as a phrase. |
UID |
[UID] |
Retrieves a biosystem record by its unique identification number, which is the numerical portion of the Accession number. For example, if an accession number is bsid12345, the corresponding UID is 12345.
If you enter a string of digits as a query and do not specify a search field, the UID field will be searched by default. |
82991[UID]
will retrieve the biosystem record whose unique identification number is 82991.
82991
will also retrieve that same biosystem record, because the UID field is searched by default for queries that are only a string of digits.
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* In a query, the field name may be typed as the full name or abbreviation, and may be in upper, lower, or mixed case. If more than one abbreviation is shown, any one of them can be used. The field name must be surrounded by square brackets []. A space between the search term and the field specifier is optional. If desired, surround a phrase with quotes to force an adjacency search. For example, the sample queries below will work equally:
"arachidonic acid"[TI]
"arachidonic acid"[TITL]
"arachidonic acid" [TITL]
"arachidonic acid" [titl]
"arachidonic acid"[Title]
** The quotes surrounding the query terms in some of the sample searches force the terms to be searched as a phrase. If quotes are not used, the Entrez system may still recognize and handle the terms as a phrase, if they are present in a phrase dictionary used by the search engine. If the terms are not present in the phrase dictionary and are not surrounded by quotes, Entrez will insert a Boolean AND between the terms; in that case, they may or may not appear adjacent to each other in the retrieved records. The "Details" folder tab on a search results page will show you exactly how the Entrez system parsed your query. More search tips are provided in the PubMed help document and Entrez help document.
It is also possible to search for a word stem by using an asterisk (*) as a wild card; for example, arachidon* will retrieve records with terms such as arachidonate, arachidonic, arachidonoyl. The Entrez Help document provides additional information about truncating search terms in this way.
![](https://webarchive.library.unt.edu/web/20201219150622im_/https://www.ncbi.nlm.nih.gov/Structure/IMG/spacer.gif)
The Entrez databases to which biosystems records have been linked (via the data processing pipeline) generally have reciprocal links from their records back to the corresponding NCBI BioSystems database records.
Therefore, if you start your search in an Entrez database other than NCBI BioSystems, you can view the "Links" menus of the records retrieved to see if they have links to associated information in the NCBI BioSystems database. Alternatively, you can use the "Find related data" menu in the right hand margin of an Entrez search results page (in whatever database you have chosen to search) and select "BioSystems" to view the associated biosystem records for all items (default) displayed on the search results page or for those you have selected using their checkboxes.
For example:
- retrieve a record for a gene or protein of interest from the Entrez Gene or Entrez Protein database, such as Gene record 5742: human PTGS1, or the protein sequence record for its gene product, NP_000953: prostaglandin G/H synthase 1 isoform 1 precursor [Homo sapiens].
- view the "Links" menu in the right margin of the Gene record, or the "Related information" menu in the right margin of the Protein record, and select "BioSystems."
- If you are looking at a Gene record, the "General Gene Information: Pathways from BioSystems" section of the record provides another way to view/link to the associated biosystems. (As an example, see GeneID 5742: human PTGS1: general gene information.)
- Click on a biosystem of interest to view its record. The gene record from which you started will appear at the top of the "genes" folder tab for that biosystem and will be selected by default (i.e., its check box will be activated). You can then click on the "Highlight selected records in source database" to view the location of the gene within the pathway diagram, if that function is available for a given biosystem. (Currently, the highlight function is available only for KEGG records and the selected gene will be displayed with a red outline, as shown in an illustrated example. The gene name will also appear in red font, as may other gene names in the pathway diagram, indicating a link to the corresponding KEGG gene record. The red outline, however, will only appear around the gene(s) that were selected in the NCBI biosystem record.)
- The biosystems that are retrieved have been associated with the gene or protein through the methods descibed in the data processing/create direct links section of the BioSystems help document.
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