**Draft Report of the Task Force on Target Tracking**

**Recommendations:**

Our committee recommends that Structural Genomics Laboratories adopt a
policy of open exchange of target information. This will allow each
laboratory to consider work in progress elsewhere as a criterion in
target selection, and help to avoid unnecessary duplication of effort.

As the simplest possible mechanism for data exchange, our committee
recommends that each Structure Genomics Laboratory maintain on its web
site a list of protein targets currently under investigation. Targets
should be described by their sequence and status-of work, using a
standard format finalized at the Airlie House meeting, as described
below.

Our committee recognizes that a central repository of target information
may be a more efficient means of data exchange. We recommend that
Structure Genomics Laboratories explore this possibility using a trial
repository, perhaps that to be developed for the NIH-funded centers.

**Background and Summary of Task Force Discussions:**

The remit of this task force was to examine mechanisms for tracking
targets for protein structure determination within the international
structural genomics community. The motivation is to make fully public
all information on what protein structures are being attempted and which
are complete, so as to assist the experimental centers world-wide in
target selection, and to provide up-to-date information to those
analyzing the results. Note that this task force activity is separate
from the NIH work on establishing tracking facilities for the NIH-funded
P50 structural genomics centers.

We considered three possible scenarios:

1\. One or more databases and associated web sites, providing
information on targets that are being attempted in the context of more
general information, such as the families to which the targets belong,
the current knowledge of structure, the models that are available.
Several sites, for example Presage and genome3D, have already begun work
in this area.

Because of the many groups who would be interested in provided such a
service, this option is very unattractive. How would the privileged
group be chosen? How would it be funded? What would happen if it were
not effective? These are all serious concerns. We feel that sharing
amongst multiple sites is also a desirable undertaking as that makes
changes in format extremely difficult and introduces complexity without
compensatory benefit.

2\. A single 'bare-bones' repository, collecting raw information from
all registered structural genomics laboratories and making it available
in a unified way. This center would not provide additional information
or services. The site manager would ensure compliance to the needed
format, information-content, and update frequency standards. The
attraction of this scenario is that no advantage would be given to the
site owners. The site would also be cheap to run. It must, however, be
extremely robust, provide archival quality data, and support those
making submissions as well as for those who wish to make use of the
data, especially "value added" sites.

The task force considers this an attractive option, assuming that a
suitable host for the site can be found.

3\. A distributed information system in which registered sites make
target information available in a standard form, accessible to anyone
via FTP. The advantage of this system is that it is a cheap, peer to
peer arrangement, involving no centralization. The disadvantage is that
it would be difficult to ensure compliance to the needed format,
information content and update frequency standards. In practice, what
might happen is that added value sites would effectively take over the
job ensuring standards are met.

The task force considers this scenario less desirable than number 2, in
principle, but it can be undertaken immediately with little effort and
may well prove an acceptable arrangement.

# Data Exchange Recommendation:

At the Airlie meeting, option 3, an exchange between web sites, was
agreed. A sample target entry in the agreed form is given below,
together with a formal XML specification of the format. Aside from the
format for an individual target entry, it was agreed that the following
associated procedures shall be followed:

1\) The targets file is a concatenation of target entries.

2\) Targets files are to be updated weekly.

3\) Each target entry represents a single protein, not a family.

4\) Target entries are not deleted. Work stopped is a status code.

5\) Each lab will communicate their targets FTP address to Steve Bryant.

6\) Labs will prepare targets files and FTP sites by 1 June 2001.

The contents of the \"sequence\" item require further explanation. The
intention is that the sequence identify the target with precision
sufficient to allow other labs to avoid unintentional duplication. For
example, when one domain of a large protein is under study, the sequence
should correspond to that domain, not the whole protein. Minor sequence
variations introduced in the course of sample preparation need not be
indicated. For example, if a domain boundary is modified slightly or HIS
tag added, the sequence need not be updated to reflect these changes.

Here is an example targets file with one target entry:

\<?xml version=\"1.0\"?\>

\<!DOCTYPE target PUBLIC \"-//Structure//target/EN\" \"target.dtd\"\>

\<target\>

\<id\>ABC123\</id\>

\<lab\>My University\</lab\>

\<date\>2001-01-01\</date\>

\<status\>Cloned\</status\>

\<status\>Expressed\</status\>

\<status\> Work Stopped\</status\>

\<sequence\>THISISMYTESTSEQ\</sequence\>

\<name\>A target example\</name\>

\</target\>

Here is the formal XML specification for target entries:

\<!ELEMENT target (id, lab, date, status+, sequence, name?, url\*,
remark\*)\>

\<!\-- required data items \--\>

\<!\-- any lab specified id \--\>

\<!ELEMENT id (#PCDATA)\>

\<!\-- any lab specified id \--\>

\<!ELEMENT lab (#PCDATA)\>

\<!\-- most recent update. format: YYYY-MM-DD \--\>

\<!ELEMENT date (#PCDATA)\>

\<!\-- status. One or more or the following descriptive terms:

Selected

Cloned

Expressed

Soluble

Purified

Crystallized

Diffraction-quality Crystals

Native diffraction-data

Phasing diffraction-data

NMR Assigned

HSQC

Crystal Structure

NMR Structure

In PDB

Work Stopped

Other \--\>

\<!ELEMENT status (#PCDATA)\>

\<!\-- protein sequence in IUPAC 1-letter codes \--\>

\<!ELEMENT sequence (#PCDATA)\>

\<!\-- optional data items \--\>

\<!\-- any lab-specified name for the protein \--\>

\<!ELEMENT name (#PCDATA)\>

\<!\-- any url of interest regarding the protein \--\>

\<!ELEMENT url (#PCDATA)\>

\<!\-- remarks in free text \--\>

\<!ELEMENT remark (#PCDATA)\>