Integrate LIMP with New Lipidat Presented by Hui Yang
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Transcript Integrate LIMP with New Lipidat Presented by Hui Yang
Integrate LIMP with
New Lipidat
Presented by
Hui Yang
Outline
Background of LIMP
Project Objectives
The procedure of integrating LIMP
with New Lipidat
What I have done so far
Future work
Background of LIMP
LIMP
LIpid/Membrane Physio-chemical
Properties Database
Alias: Vadim’s data
The original form of LIMP is in
spreadsheet
Vadim produces LIMP data in
spreadsheet-form
These data are grouped into different
workbooks
LIMP in spreadsheet-form (1)
1. lipids
Lipid
ID #
MSDB
ID # M.wt. Type
1
pl
2
pl
Headgr Head
oup group
1
2
Chain
1
pc
16:0
pc
14:0
Ch Ch
ain ain Bkbn Bkbn
3 4 1
2
gro
gro
Chain
2
16:0
14:0
Lipid
Name
1,2-Dipalmitoyl-sn-glycero-3-phosphocholine
1,2-Dimyristoyl-sn-glycero-3-phosphocholine
2. Natural
Lipids
Head Head
Nat
Lip
ID#
Lipid
Source
Type
(mx, lx, tx,
wo,nr)
9999 text
text
1 egg yolk lx
Abbreviatio
n
DPPC
DMPC
Chai
Headgroup group group Chain
n
restriction restri restri restriction restri
1
ction ction 1
ction
Chai
n
restr Backbn
ictio restriction Lipid Type
text
pc
text text
text
text
text
text
text
pl
3. Non Lipids
Non-lipid
ID#
Non-lipid
name
type
9999 text
text
1 peptide16 peptide
Non-lipid Fn
text
16 leucines bounded by two lysines at both end
LIMP in spreadsheet-form (2)
4. Media
Wate
r (H, H2O
name
Medium D,
content non- for nonID#
HD) , %
aqua aqua1 cont
9999 text
1H
2H
9999 text
text
text
name
name
for nonfor nonconc1
aqua2 cont aqua3 cont Comp1 conc 1 units Comp2
con
c4
conc2
conc3 Com conc unit Co con
4
s
mp5 c 5
conc 2 units
Comp3 conc 3 units p4
text
text
text text
text text
PIPES
text
text
text
5 mM
KCl
text
text
text
text
text
text text text text
200 mM
5. Sample
Lipid Lipid Lipid1
Sample 1 ID 1
purity Lipid 1
ID#
#
purity method source
9999 9999 text
1
2
2
3
text
text
Avanti
Avanti
Nat
Lipid 1 Non- NonNat Lipid Nat Lipid purity
lipid 1 lipid 1
1 ID #
1 purity method ID # purity
9999 text
text
9999 text
Nonlipid 1 Nonpurity
lipid 1 Concen Sample Media Media
method source tration fn
ID # content
Med
content
units,
%w/w
Aggr.
State
text
text
text
text
text
text
9999 text
1 excess
1 excess
luv
luv
LIMP in spreadsheet-form (3)
6. Method
Method ID#
9999
1
2
Method
text
GX
PA
7. Data
M
Data
Meth eTemper
Record Biblio Sample 1
tature, Pres
ID#
ID# ID#
ID# hoC
sure
99991 9999
1966 99991 99992 text 29 text
48 1950
20
4
30
59 1951
26 14
20
63 1957
30 10
24
Osmotic
Pressure,
dyne/cm2
text
Relative
Humidity
,%
Phase Other1
text
text L text
L
L
L'
Other2
text
therm_a
mol_
area
vol
therm rea
area units therm _area units,
mol_vol units
2
o area err (Å ) _area err 1E-3 C mol_vol err (Å3) spec_vol
9999 9999 text 9999 9999
text 9999 9999 text
9999
69.4 1.2
0.9883
47.9 0.2
1148
2
Features of LIMP
(spreadsheets)
Self-contained
Some data already exist in New Lipidat
Some data has same structure with data
in New Lipidat
Most synthetic lipids / natural lipids
Media
methods
All LIMP samples
New data
Attributes of data
All data records in ‘Data’
Relationship in LIMP (spreadsheet)
LipCom
V_Lipid_id
New
!
New
!
Sample
Data
V_sample_id
V_data_id
NaturalLip
V_Lipid_id
V_sample_id
V_natural_Lipid_id
V_natural_lipid_id
{Attribute_id}
V_non_lipid_id
V_method_id
NonLipid
V_non_Lipid_id
Attributes
Attribute_id
New
!
V_media_id
Methods
V_method_id
Media
V_media_id
LIMP and New Lipidat
LIMP
(spreadsheet)
Old Lipidat
Migration/conversion
Lipidag
LIMP
New Lipidat
LIPIDAT: phase
transition data
INTEGRATION
Shared data:
Lipids/media/
methods/biblio
Lipidat
conversion
LIMP
LIMP: non-phase
transition data
The build-up of LIMP
Phase 1:
Collect data
Spreadsheet-form
LIMP
Transform LIMP from spreadsheet-form to
Phase 2: database-form
Vadim
Hui
Integrate LIMP with New Lipidat
Phase 3: Web-based search on LIMP
Future
Project objectives
Transform LIMP from spreadsheetform to database-form
Integrate LIMP with New Lipidat
Generalize the integration
procedure
All workbooks have same structure
Apply the same integration procedure
to all workbooks
Steps needed
Pre-steps:
get familiar with:
Chemistry terms
Database structures (New Lipidat, LIMP)
Access 2000
Transform LIMP from spreadsheet-form into
database form
Design and implement the procedure for
integrating LIMP with New Lipidat
Generalize the procedure
Encapsulate all the steps involved in incorporation into
one unit so that they can apply to all Vadim’s workbooks
Transforming(ExcelAccess)
Use Access’ “import” utility
Procedure of integration (1)
Lipids,Natural Lipids, Media (shared data)
Determine lipid_id in New Lipidat for each
LIMIP lipid by matching type,HGs,BBs and
Chains
Determine natural_lipid_id in New Lipidat for
each natural lipid
Determine media_id in New Lipidat for each
medium
Procedure of integration (2 )
Append LIMP ‘sample’ to the ‘sample’
table in New Lipidat, using the
lipid_id,natural_lipid_id and media_id
obtained in the above step.
Procedure of integration (3)
LIMP-specific data
Attributes of LIMP data
LIMP data
Create a new table
Populate attributes from the first workbook
Add new attributes if a new one appears
Create a new table for LIMP data
Get LIMP data from Vadim’s workbooks
Adding them to this table
Verify all the above steps are correct
Match LIMP lipids with existing
Lipids
Convert spreadsheet-form “lipids” into an
Access2000 table
Check if there are new headgroups, new
backbones,new chains and new lipids,if yes, put
all these new items in a report
Submit the report to Professor Kerr, make sure
they are not caused by incomplete data in New
Lipidat
Submit the report to Vadim, let Vadim determine
if they are really new ones or typos
Append these new items into different tables
after Vadim’s check
Lipid Matching (1)
Lipid in Vadim’s Workbook
V_Lipid_id
type
20
pl
headgroup
pc
backbone
chain
gro
1-16:0
Example2: lipids matching
Lipid in New Lipidat
Lipid_type
type_ID
TYPE
3
pl
Lipid_to_headgroup
Lipid_id
3
lipids
type
LIPID_ID
TYPE_ID
3
3
pl
Lipid_id
Hg_id
3
108
headgroup
headgroups
Hg_id
headgroup
108
pc
backbone
backbones
Lipid_to_backbone
pcLipid_id
3
bb_id
gro
8
chain
1-16:0
backbone
bb_id
8
gro
chains
Lipid_to_chains
Lipid_id
chain_id
Chain_id
chain
3
1
1
1-16:0
Lipid Matching (summary)
lipids
Lipid_to_hg
headgroups
Lipid_to_bb
backbones
Lipid_to_ch
chains
New Lipidat
assembling
Existing Lipids
( same structure as Vadim’s lipids)
disassembling
Vadim’s Lipids
Match them
Append new items into New Lipidat
Report For Workbook1
new headgroups found in Workbook1
lipid ID#
Headgroup 1
24
pe-Me
25
pe-Me2
New chain found in Workbook1
v_lipid_id
ch1
48
16:1
Report for Workbook1
New LIPIDS found in Workbook1
v_lipid_id
new_lipid_id
Type
hg1
37
hg2
-1
pl
pe
XXXX
38
-1
gl
glc
39
-1
gl
glc
ch1
ch2
ch3
ch4
bb1
bb2
n
XXXX
XXXX
XXXX
gro
XXXX
XXXX
O-10:0
O-10:0
XXXX
XXXX
gro
XXXX
XXXX
O-12:0
O-12:0
XXXX
XXXX
gro
XXXX
Process LIMP “data”
Vadim’s data have dozens of attributes, in
workbook1, there are 26 attributes.
The number of attributes is changing, maybe,
there will be over 100 attributes at last
There are two methods dealing with these
varying attributes
Queries:
Easy to implement
need change queries whenever a new attribute comes out
Programming:
Flexible, no change needed in case of new attributes’
occurrence
Harder to implement
Verify the above steps
The verification method
Generate “r_sample” and “r_data”
reports using the data in New
Lipidat.Those two reports have same
structure with Vadim’s “sample” and
“data” spreadsheets
compare:
“r_sample” and “sample”
“r_data” and “data”
What I have done(1)
Finish all the pre-steps
Chemistry
Database Structure
Access2000
Publish Vadim’s workbook1 on web
Write an article which describes how to
convert an Excel spreadsheet into an
Access2000 table
Finish the phase of ‘lipids matching’
What I have done (2)
Finish the phase of ‘lipids matching’
Finish creating all new tables
required by LIMP
Append partial sample data
(synthetic lipids) into New Lipidat
Future Work
Finish the matching for ‘natural_lipids’
and ‘media’
Write queries to insert LIMP data
Generate reports to verify all the
incorporation steps
Encapsulate all the steps into one unit
? Write a program to process LIMP
‘data’—changing attributes
Acknowledgements
Thank You!
Example1 (self-contained)
Lipid_id
type
Hg1
bb1
ch1
1
Method_id
method
1
Medium_id
GX
content
1
Sample_id
Lipid_id
Media_id
1
1
1
Data_id
sample_id
method_id
1
1
1
attr1
attr2