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3.4 General elements and tags |
The elements described in this section are the additional bits and pieces
necessary to describe a biopolymer. For example, a particular gene may have
been first described in a journal article. Therefore, there should be a <reference>
element that can be associated with that gene to point to that description. A
protein may be a part of in a specific <organism>, which should be
described using standard taxonomy.
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3.4.1 General-purpose elements |
These elements are generally leaves rather than branches: they can be
associated with almost any other element and they are used to attribute
descriptive names and information with that element.
| Element |
Attributes |
Functions |
| name |
— |
A text name for an enclosing element |
| alt_name |
order |
A text alternate name for an enclosing element |
| note |
id
order |
Text describing an enclosing element |
| comment |
— |
Text describing the BIOML code. This element should
be ignored by any browser. |
| copyright |
— |
The copyright declaration for a BIOML file. |
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3.4.2 Organism-identifying elements |
These elements are for use in describing the organism that a biopolymer is was
a part of originally. The organism tags will surround the biopolymer tags,
because the biopolymer is part of the organism, not vice versa.
| Element |
Attributes |
Functions |
| organism |
id
type |
Encloses the specification of an organism |
| species |
id |
Encloses the genus and species for an organism |
| common_name |
— |
The common name for the organism |
| alt_common_name |
— |
An alternative common name for the organism |
| taxon |
id
type |
A specification of any additional, relavent taxonomy |
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3.4.3 Location elements |
These elements describe where a protein is located within an organism, that is
they allow the specification of tissue, cell type, and subcellular organelle
inwhich a particular protein is found. These tags also logically enclose the
protein. Nucleic acids do not require this type of specification, because there
location is fixed in the nucleus for DNA and it is irrelavent biologically for
mRNA.
| Element |
Attributes |
Functions |
| tissue |
id
type |
Encloses the specification of a tissue type |
| cell |
id
type |
Encloses the specification of a cell type |
| organelle |
id
type |
Encloses the specification of an organelle type |
| particle |
id
type |
Encloses the specification of a particle type |
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3.4.4 Literature references |
The purpose and use of these tags is self-evident. All of the elements other
than <reference> are leaves of reference and they only have
meaning when they are enclosed by <reference> ... </reference>tags.
| Element |
Attributes |
Functions |
| reference |
id |
Encloses a literature reference |
| author |
— |
One of the authors, e.g., "Beavis RC" |
| title |
— |
Title of the reference |
| journal |
— |
Name of the journal that published the article |
| book_title |
— |
Title of the book containing the article |
| editor |
— |
An editor of the appropriate book |
| volume |
— |
Number of the journal volume
or book in series |
| pages |
— |
The article page numbers |
Writing down the details of a reference using these elements is one way to deal
with the problem of adding literature attributions to a file. An alternate
method, which is very effective and compact is to use the Medline reference
number for a particular reference and leave the details out of the BIOML file
altogether:
<reference>
<db_entry format="MEDLINE" entry="80120725">
</reference>
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3.4.5 Database reference |
Most of the information about biopolymers is currently held in large
computerized databases, which is the driving force behind the development of
BIOML. These elements allow BIOML to capture information about databases and
make reference to them. The <db_entry/> element and its attributes id,
ac,format, and query are used to make reference to a
particular database entry. query is a of the Universal Resource Locator
(URL) for a copy of a database and a properly formatted query string that would
allow a database entry to be retrieved by an HTTP or FTP network request. This
element is a special case of the general <query/>. <db_entry/>
elements are always empty element described in the next section.
| Element |
Attributes |
Functions |
| db_entry |
id
name
entry
format
query |
A reference to a database entry |
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3.4.6 URL-based resources |
These elements point to specific resources available by a network protocol such
as FTP or HTTP. These resources can either be in the form of a particular <file/>
held on a remote server, or it can be a request for a particular piece of
information using a Common Gateway Interface (CGI) style <query/>.
Both of these elements are always empty.
| Element |
Attributes |
Functions |
| file |
format
URL |
An element pointing to a file |
| query |
format
query
query_string |
An element querying to a server program |
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3.4.7 Binary data |
These element types allow the inclusion of blocks of formatted data. The data
can be in any one of a number of formats, such as GZIP or ZIP compressed, JPEG
or GIF formatted graphical information, or any other type of binary data.
Elements within <binary> tags will necessarily be only
understandable by a computer. <data> tags enclose formatted text data
that has a strict, agreed upon format, for example, PDB format atomic
co-ordinates.
| Element |
Attributes |
Functions |
| binary |
format
length |
An element enclosing formatted binary information |
| data |
format
length |
An element enclosing formatted text information |
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3.4.8 Forms |
One of the strengths of HTML in its current incarnation is the inclusion of
elements that allow a programmer to create "fill-in-the-blanks" forms that are
used to communicate with HTTP server-side programs. BIOML also includes a set
of elements for laying out simple forms that can be used to send information to
server programs.
| Element |
Attributes |
Functions |
| form |
type
action |
An element enclosing a form |
| input |
type
name
value
width |
An element allowing the input of data |
| text |
— |
An element enclosing text to be inserted into the
form |
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3.4.9 Global attributes and entities |
There are some attributes that may be included with any element, but which have
not been listed individually above, to prevent repetition. These attributes are
as follows:
| Element |
Attributes |
Functions |
| All |
label |
This attribute provides a text identifier for a
particular element that can be used by a browser as a place-holder for that
element
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| All |
state |
This attribute provides a browser with a hint as to
how to display a particular element |
| All |
id |
This attribute provides a browser with a number to
use for cataloging an element |
Entities are globally available mnemonics for characters and combinations of
characters that are either not available on standard keyboards or which would
confuse a browser. For example, the presence of quotations marks, ampersands
and right and left angle brackets can confuse browsers. These symbols should be
replaced by the entities listed below when they occur in text, as opposed to
when they occur in tag specifications. Entities all follow the general format
of &xxx; where the xxx is the replacement mnemonic.
| Symbol |
Entity |
Symbol |
Entity |
| & |
& |
< |
< |
| " |
"e; |
> |
> |
| © |
©right; |
® |
®istered; |
| — |
&emdash; |
– |
&endash; |
| ± |
&plusminus; |
° |
°ree; |
| Å |
&angstrom; |
ASCII character |
&#int;
(int=decimal equivalent) |
| new line |
&newline; |
new paragraph |
¶graph; |
| • |
• |
new bulleted point |
&point; |
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3.3 Protein-specific elements
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TOC
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4. Extending BIOML
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