**[New Features in IMG 2.3 Web UI]{.underline}**

(July 9, 2007)

Some changes have been made to the IMG 2.3 Web UI:

-   Uploading Gene Cart feature is moved to the Gene Cart page (from
    MyIMG).

-   Uploading Function Cart feature is moved to the Function Cart page
    (from MyIMG).

-   Parts lists can be organized into Function Network.

-   MyIMG annotations have been enhanced.

-   Some additional attributes have been added.

# 1. Uploading Gene Cart

"Upload Gene Cart from File" feature is now in the Gene Cart page. Click
the "Upload Gene Cart" button to upload gene cart contents from a file.
Flat file format for gene cart upload remains the same as in IMG 2.2 and
before.

![](media/image1.png){width="5.99375in" height="5.677777777777778in"}

(Figure 1.1: New Gene Cart with "Upload Gene Cart" button)

# 2. Uploading Function Cart

"Upload Function Cart from File" feature is now in the Function Cart
page. Click the "Upload Function Cart" button to upload function cart
contents from a file. Flat file format for function cart upload remains
the same as in IMG 2.2 and before.

![](media/image2.png){width="5.997222222222222in"
height="5.082638888888889in"}

(Figure 2.1: New Function Cart with "Upload Function Cart" button)

# 3. Function Networks, Pathways and Parts Lists

The new Function Networks in IMG 2.3 can contain pathways and/or parts
lists.

## 3.1 Browsing Networks, Pathways and Parts Lists

In IMG 2.2 and before, networks and pathways are all listed under "IMG
Pathway" based on the network-pathway hierarchical structure. In the new
IMG 2.3 UI:

-   Function Network: show function network hierarchy with pathways and
    parts lists;

-   IMG Pathway: list IMG pathways in alphabetical order;

-   IMG Parts List: list IMG parts lists in alphabetical order.

![](media/image3.png){width="5.992361111111111in"
height="5.840277777777778in"}

(Figure 3.1: New IMG 2.3 UI with "Function Network," "IMG Pathway" and
"IMG Parts List")

Function Network Browser page (Figure 3.2) shows the Function Network
hierarchy with pathways and parts lists.

![](media/image4.png){width="5.998611111111111in"
height="6.379861111111111in"}

(Figure 3.2: Function Network Browser)

Click on a function network hyperlink, the function network detail,
together with pathways and parts lists in this network, will be
displayed in a new page.

![](media/image5.png){width="5.998611111111111in"
height="6.613888888888889in"}

(Figure 3.3: Function Network Detail page)

IMG Pathways page (Figure 3.4) lists all pathways in alphabetical order.

![](media/image6.png){width="5.998611111111111in"
height="6.379861111111111in"}

(Figure 3.4: IMG Pathways page)

IMG Parts List page (Figure 3.5) lists all parts lists in alphabetical
order.

![](media/image7.png){width="5.998611111111111in"
height="6.379861111111111in"}

(Figure 3.5: IMG Parts List page)

## 3.2 Assigning Parts Lists to Network Hierarchy

The new Update IMG Parts List page (Figure 3.6) allows users to specify
to which network(s) this parts list belong.

![](media/image8.png){width="5.998611111111111in"
height="6.613888888888889in"}

(Figure 3.6: Update IMG Parts List page)

Click to select network(s) in the "Function Network Selection" section,
then click the "Update" button. The current parts list will be assigned
to the selected network(s).

# 4. MyIMG Annotations

IMG 2.3 expands MyIMG annotations from "product name only" annotation to
user annotations of the following properties:

-   Product Name

-   Prot Desc

-   EC Number

-   PUBMED ID

-   Inference

-   Is Pseudo Gene?

-   Notes

## 4.1 View MyIMG Annotations on a Gene

Users can view their own annotations on a gene in the **[Gene
Detail]{.underline}** page (Figure 4.1 and Figure 4.2).

![](media/image9.png){width="5.999305555555556in"
height="5.622222222222222in"}

(Figure 4.1: **[Gene Detail]{.underline}** page)

![](media/image10.png){width="5.999305555555556in"
height="5.622222222222222in"}

(Figure 4.2: **[Gene Detail]{.underline}** page with MyIMG Annotation)

Click on the "Show All User Annotations" button, **[All User Annotations
on Gene nnnnnnnnn]{.underline}** (Figure 4.3) will be displayed. User's
own annotation (if any) will be displayed in the first line. Different
annotations by other users are displayed in red for easy comparisons.

![](media/image11.png){width="5.996527777777778in"
height="6.086805555555555in"}

(Figure 4.3: **[All User Annotations on Gene]{.underline}** page)

## 4.2 Enter or Delete MyIMG Annotations

Users can enter, modify or delete MyIMG annotations on genes. To enter
or update MyIMG annotation on one or more genes, first add the gene(s)
to the Gene Cart, and then click the "Annotate Selected Genes" button in
the Enter MyIMG Annotation section (Figure 4.4).

![](media/image12.png){width="5.993055555555555in"
height="6.200694444444444in"}

(Figure 4.4: **[Gene Cart]{.underline}** page with "Annotate Selected
Genes" button)

In the **[MyIMG Annotation for Selected Genes]{.underline}** page
(Figure 4.5), all selected genes from the Gene Cart will be displayed.

![](media/image13.png){width="5.993055555555555in"
height="6.4527777777777775in"}

(Figure 4.5: **[MyIMG Annotation for Selected Genes]{.underline}** page)

Users can select a gene OID in the "Upload existing MyIMG annotation for
gene" listbox and click "Load Gene Annotation" button to fill in the
form with existing annotations.

To enter or update MyIMG annotation on the selected genes, simply edit
the text in each field, and then click the "Update Annotation" button to
perform database update.

To delete existing annotations, simply click the "Delete Annotation"
button.

Note that only selected genes will have their annotations updated or
deleted.

## 4.3 View All MyIMG Annotations

To view annotations on more than one gene, select the "MyIMG" tab, and
then select the "Annoations" sub-tab. A new **[IMG User
Annotations]{.underline}** page (Figure 4.6) will be displayed.

![](media/image14.png){width="5.998611111111111in"
height="6.566666666666666in"}

(Figure 4.6: **[IMG User Annotations]{.underline}** page)

To view your own annotations, click the "View My Annotations" button,
the following **[My Annotations]{.underline}** page (Figure 4.7) will be
displayed.

![](media/image15.png){width="5.990972222222222in"
height="6.147222222222222in"}

(Figure 4.7: **[My Annotations]{.underline}** page)

Users can select genes to add to Gene Cart for further annotation (by
clicking "Add to Gene Cart" buttin), or can export annotations to Excel
(by clicking "Export Annotations" button).

## 4.4 View Annotations per User

To view annotation summary per user, click the "View Annotations by
Users" button, the following **[All User Annotations]{.underline}** page
(Figure 4.8) will be displayed.

![](media/image16.png){width="5.990972222222222in"
height="6.147222222222222in"}

(Figure 4.8: **[All User Annotations]{.underline}** page)

Click any number in the "Genomes" column, the following **[Genomes with
Annotations by User xxxx]{.underline}** page (Figure 4.9) will be
displayed, showing all genomes that have genes annotated by
corresponding user xxxx.

![](media/image17.png){width="5.995833333333334in"
height="5.535416666666666in"}

(Figure 4.9: **[Genomes with Annotations by User]{.underline}** page)

Click any number in the "Genes" column, the following **[Annotations by
User xxxx]{.underline}** page (Figure 4.10) will be displayed, showing
all genes annotated by corresponding user xxxx.

![](media/image18.png){width="5.995833333333334in"
height="6.753472222222222in"}

(Figure 4.10: **[Annotations by User]{.underline}** page)

To view and comparison annotations by two or more users, first select
those users, and then click the "View User Annotations" button on the
**[All User Annotations]{.underline}** page (Figure 4.8). The following
**[Selected User Annotations]{.underline}** page (Figure 4.11) will show
up. All genes that have been annotated by any selected users will be
displayed on this page. The display is sorted on Gene Object ID values.
Repeated entries (i.e., same genes annotated by different users) will
have Gene OID values shown in magenta for easy comparison (Figure 4.12).

![](media/image19.png){width="5.992361111111111in"
height="6.388888888888889in"}

(Figure 4.11: **[Selected User Annotations]{.underline}** page)

![](media/image20.png){width="5.992361111111111in"
height="6.388888888888889in"}

(Figure 4.12: **[Selected User Annotations]{.underline}** page with
"repeat entries")

## 4.5 View Annotations per Genome

To view annotation summary per user, click the "View Annotations by
Genomes" button, the following **[All Genome Annotations]{.underline}**
page (Figure 4.13) will be displayed.

![](media/image21.png){width="5.992361111111111in"
height="6.388888888888889in"}

(Figure 4.13: **[All Genome Annotations]{.underline}** page)

Click any numbers in the "Gene" column, the following **[View
Annotations]{.underline}** page (Figure 4.14) will show up, listing all
genes in this genome that have user annotations. Users can select genes
to add to Gene Cart for annotations.

![](media/image22.png){width="5.992361111111111in"
height="6.388888888888889in"}

(Figure 4.14: **[View Annotations]{.underline}** page)

Click any number in the "users" column, the following page (Figure 4.15)
will be displayed showing all users who have annotated any genes in this
genome.

![](media/image23.png){width="5.995833333333334in"
height="5.535416666666666in"}

(Figure 4.15: Page showing all users who have annotated genes in a
particular genome)

To view annotations on genes in different genomes, first select those
genomes, and then click the "View Annotations on Genome(s)" button on
the **[All Genome Annotations]{.underline}** page (Figure 4.13). The
following **[Selected Genome Annotations]{.underline}** page (Figure
4.16) will show up. All genes in the selected genomes that have MyIMG
annotations will be displayed on this page. The display is sorted on
Gene Object ID values. Repeated entries (i.e., same genes annotated by
different users) will have Gene OID values shown in magenta for easy
comparison.

![](media/image24.png){width="5.991666666666666in"
height="6.098611111111111in"}

(Figure 4.16: **[Selected Genome Annotations]{.underline}** page)

## 4.6 Download MyIMG Annotations

Users can download their own annotations to an Excel file. In order to
export annotations, go to the **[My Annotations]{.underline}** page
(Figure 4.7), select one or more genes, and then click the "Export
Annotations" button. The selected gene annotations will be exported to
an Excel file. The file will have the following columns:

-   gene_oid: Gene Object ID;

-   MyIMG_Annotation: annotated product name;

-   MyIMG_Prot_Desc: annotated prot desc;

-   MyIMG_EC_Number: annotated enzyme EC number(s);

-   MyIMG_PUBMED_ID: annotated PUBMED ID(s);

-   MyIMG_Inference: annotated inference;

-   MyIMG_Is_Pseudogene: is pseudo gene?

-   MyIMG_Notes: user annotated free text notes.

## 4.7 Upload MyIMG Annotations from Flat File

Users can upload MyIMG annotations from a tab-delimited flat file. The
file will have the same column header as the exported Excel file (see
Section 4.6). Only "gene_oid" and "MyIMG_Annotation" columns are
required. Others are optional.

In order to perform the file upload, first go to **[IMG User
Annotations]{.underline}** page (Figure 4.6), and click the "Upload
Annotations" button. The following **[Upload MyIMG Annotations from
File]{.underline}** page (Figure 4.17) will show up.

![](media/image25.png){width="5.991666666666666in"
height="5.616666666666666in"}

(Figure 4.17: **[Upload MyIMG Annotations from File]{.underline}** page)

Enter the file name or use "Browse ..." to find the file to upload, and
then click the "Open" button. The file will be parsed and validated
first. The validation process will check:

-   Whether the file contains "gene_oid" and "MyIMG_Annotation" columns;

-   Whether gene_oid exists;

-   Whether EC numbers are in correct format;

-   Whether PUBMED ID values are integers;

-   Whether the MyIMG_Is_Pseudogene field value is 'Yes', 'No' or
    'Unknown'.

Figure 4.18 shows an example **[File Validation Result]{.underline}**
page with error messages. Users can correct any errors in the file and
validate again, or they can click the "Upload" button to perform the
actual upload.

![](media/image26.png){width="5.992361111111111in"
height="4.701388888888889in"}

(Figure 4.18: **[File Validation Result]{.underline}** page)

## 4.8 Set MyIMG Preferences

Users can select to whether override Gene Display Name in the Web UI
using their own annotated product names. To set this preference, go to
the "Preferences" sub-tab in the "MyIMG" tab. There is a new "MyIMG
Preference" section (Figure 4.19). If the item is "checked", then user
annotated product names will override gene product name displays in IMG.
Click the "Save MyIMG Preference to Database" button to apply and to
save the change. Since the preference is saved in the IMG database,
users don't have to reset this option everytime.

(*[Question: Do we also override "Is Pseudo Gene"?]{.underline}*)

![](media/image27.png){width="5.998611111111111in"
height="6.613888888888889in"}

(Figure 4.19: **[Preferences]{.underline}** page)

## 4.9 Output Genbank File with MyIMG Annotations

The existing "Output Genbank File" feature is revised to include the new
MyIMG annotation options such as EC_Number and PUBMED ID. Users can
select whether to include their own annotations in the Genbank file or
not.

The mapping from MyIMG annotations to Genbank properties are as follows:

-   MyIMG_Annotation (or annotated product name)  replacing /product

-   MyIMG_Prot_Desc (or annotated prot_desc)  /prot_desc

-   MyIMG_EC_Number  replacing /EC_Number

-   MyIMG_PUBMED_ID  /db_xref

-   MyIMG_Inference  /inference

-   MyIMG_Is_Pseudogene  replacing /pseudo

-   MyIMG_Notes  /note

*[Question: Do we need output EMBL files?]{.underline}*

# 5. Additional Attributes

Additional attributes have been added to several object classes.

## 5.1 IMG_Term with Enzyme EC Numbers

In IMG 2.2 and before, enzyme EC numbers were embedded in the IMG terms.
In IMG 2.3, enzyme EC numbers are explicitly stored in a separate
set-valued attribute.

The following **[Update IMG Term Page]{.underline}** (Figure 5.1) shows
an IMG term with 2 enzyme EC numbers:

![](media/image28.png){width="5.997916666666667in"
height="5.184722222222222in"}

(Figure 5.1: New **[Update IMG Term Page]{.underline}** with "EC
Number(s)")

EC numbers are entered in the "EC Number(s)" text field. If there are
two or more EC numbers for the same term, use blank to separate them.

## 5.2 IMG_Reaction Reaction Type

A new "Reaction Type" attribute has been added to IMG_Reaction class.
Reaction type is a free text field.

![](media/image29.png){width="5.997916666666667in"
height="5.184722222222222in"}

(Figure 5.2: New **[Add IMG Reaction Page]{.underline}** with "Reaction
Type")

## 5.3 Sub-cell Localization IMG Reaction-Compound

A new "Sub-cell Localization" attribute has been added to IMG
Reaction-Compound associations (Figure 5.3). Sub-cell Localization
values are selected from a pre-defined drop-down list.

![](media/image30.png){width="5.9944444444444445in"
height="5.6305555555555555in"}

(Figure 5.3: New **[IMG Reaction -- Compound Curation
Page]{.underline}** with "Sub-cell Localization")

## 5.4 Sub-cell Localization IMG Term - Reaction

A new "Sub-cell Localization" attribute has been added to IMG Term --
Reaction associations (Figure 5.4). Sub-cell Localization values are
selected from a pre-defined drop-down list.

![](media/image31.png){width="6.0152777777777775in"
height="5.322916666666667in"}

(Figure 5.4: New **[IMG Term - Reaction Curation Page]{.underline}**
with "Sub-cell Localization")