CLIR Synchronous Session: DataUp

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Carly Strasser California Digital Library @carlystrasser May 14 2013 CLIR Synchronous Session DataUp: Helping manage & archive data From Flickr by Spatial Mongrel

description

Presentation for CLIR postdocs in data curation on 14 April 2013.

Transcript of CLIR Synchronous Session: DataUp

Page 1: CLIR Synchronous Session: DataUp

Carly&Strasser&&California&Digital&Library&&@carlystrasser&

May&14&2013&CLIR&Synchronous&Session&&

DataUp:&&Helping&

manage&&&archive&data&&

From%Flickr%by%Spatial%Mongrel%

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Roadmap&

1. Background&&

2. The&DataUp&project&

3. Questions&

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Population0Dynamics0of0the0Softshell0clam,0Mya$arenaria&

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Cape%Cod%Bay%

Boston%Harbor%

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Genetics&

Shell&chemistry&

Math&

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From%Flickr%by%Mitmensch0812%

Academia?&Teaching?&Publishing?&

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NSF&funded&DataNet&Project&Office&of&Cyberinfrastructure&

Two0main0goals:01.  Build0a0network0for0data0repositories02.  Build0community0around0data0

Focus&on&&Earth0|0environmental0|0ecological0|0oceanographic00

data&&

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Why0don’t0people0share0data?0

Is0data0management0being0taught?0Do0attitudes0about0

sharing0differ0among0disciplines?0

How0can0we0promote0storing0data0in0repositories?0

What0barriers0to0sharing0can0we0eliminate?0

What0role0can0libraries0play0in0data0education?0

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Roadmap&

1. Background&&

2. The&DataUp&project&

3. Questions&

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Why&is&data&management&&&a&hot&topic?&

From%Flickr%by%Velo%Steve%

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Back in the day…

Da%Vinci%

Curie%

Newton%

classicalschool.blogspot.com%

Darwin%

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Digital0data0From

%Flickr%by%Flickm

or%

From

%Flickr%by%US%Arm

y%En

vironm

ental%C

omman

d%

From

%Flickr%by%%DW08

25%

C.%Strasser%

Courtesey%of%W

HOI%

From

%Flickr%by%%deltaMike%

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Digital0data0+00

Complex0workflows0

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C:\Documents and Settings\hampton\My Documents\NCEAS Distributed Graduate Seminars\[Wash Cres Lake Dec 15 Dont_Use.xls]Sheet1Stable Isotope Data Sheet

Wash Cresc Lake Peter's lab Don't use - old dataAlgal Washed RocksDec. 16Tray 004

SD for delta 13C = 0.07 SD for delta 15N = 0.15

Position SampleID Weight (mg) %C delta 13C delta 13C_ca %N delta 15N delta 15N_ca Spec. No.A1 ref 0.98 38.27 -25.05 -24.59 1.96 4.12 3.47 25354A2 ref 0.98 39.78 -25.00 -24.54 2.03 4.01 3.36 25356A3 ref 0.98 40.37 -24.99 -24.53 2.04 4.09 3.44 25358A4 ref 1.01 42.23 -25.06 -24.60 2.17 4.20 3.55 25360 Shore Avg ConA5 ALG01 3.05 1.88 -24.34 -23.88 0.17 -1.65 -2.30 25362 c -1.26 -27.22A6 Lk Outlet Alg 3.06 31.55 -30.17 -29.71 0.92 0.87 0.22 25364 1.26 0.32A7 ALG03 2.91 6.85 -21.11 -20.65 0.48 -0.97 -1.62 25366 cA8 ALG05 2.91 35.56 -28.05 -27.59 2.30 0.59 -0.06 25368A9 ALG07 3.04 33.49 -29.56 -29.10 1.68 0.79 0.14 25370A10 ALG06 2.95 41.17 -27.32 -26.86 1.97 2.71 2.06 25372B1 ALG04 3.01 43.74 -27.50 -27.04 1.36 0.99 0.34 25374 cB2 ALG02 3 4.51 -22.68 -22.22 0.34 4.31 3.66 25376B3 ALG01 2.99 1.59 -24.58 -24.12 0.15 -1.69 -2.34 25378 cB4 ALG03 2.92 4.37 -21.06 -20.60 0.34 -1.52 -2.17 25380 cB5 ALG07 2.9 33.58 -29.44 -28.98 1.74 0.62 -0.03 25382B6 ref 1.01 44.94 -25.00 -24.54 2.59 3.96 3.31 25384B7 ref 0.99 42.28 -24.87 -24.41 2.37 4.33 3.68 25386B8 Lk Outlet Alg 3.04 31.43 -29.69 -29.23 1.07 0.95 0.30 25388B9 ALG06 3.09 35.57 -27.26 -26.80 1.96 2.79 2.14 25390B10 ALG02 3.05 5.52 -22.31 -21.85 0.45 4.72 4.07 25392C1 ALG04 2.98 37.90 -27.42 -26.96 1.36 1.21 0.56 25394 cC2 ALG05 3.04 31.74 -27.93 -27.47 2.40 0.73 0.08 25396C3 ref 0.99 38.46 -25.09 -24.63 2.40 4.37 3.72 25398

23.78 1.17

Reference statistics:

Sampling Site / Identifier:Sample Type:

Date:Tray ID and Sequence:

From%Stephanie%Hampton%(2010)% %%ESA%Workshop%on%Best%Practices%

20tables0

From%Stephanie%Hampton%

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C:\Documents and Settings\hampton\My Documents\NCEAS Distributed Graduate Seminars\[Wash Cres Lake Dec 15 Dont_Use.xls]Sheet1Stable Isotope Data Sheet

Wash Cresc Lake Peter's lab Don't use - old dataAlgal Washed RocksDec. 16Tray 004

SD for delta 13C = 0.07 SD for delta 15N = 0.15

Position SampleID Weight (mg) %C delta 13C delta 13C_ca %N delta 15N delta 15N_ca Spec. No.A1 ref 0.98 38.27 -25.05 -24.59 1.96 4.12 3.47 25354A2 ref 0.98 39.78 -25.00 -24.54 2.03 4.01 3.36 25356A3 ref 0.98 40.37 -24.99 -24.53 2.04 4.09 3.44 25358A4 ref 1.01 42.23 -25.06 -24.60 2.17 4.20 3.55 25360 Shore Avg ConA5 ALG01 3.05 1.88 -24.34 -23.88 0.17 -1.65 -2.30 25362 c -1.26 -27.22A6 Lk Outlet Alg 3.06 31.55 -30.17 -29.71 0.92 0.87 0.22 25364 1.26 0.32A7 ALG03 2.91 6.85 -21.11 -20.65 0.48 -0.97 -1.62 25366 cA8 ALG05 2.91 35.56 -28.05 -27.59 2.30 0.59 -0.06 25368A9 ALG07 3.04 33.49 -29.56 -29.10 1.68 0.79 0.14 25370A10 ALG06 2.95 41.17 -27.32 -26.86 1.97 2.71 2.06 25372B1 ALG04 3.01 43.74 -27.50 -27.04 1.36 0.99 0.34 25374 cB2 ALG02 3 4.51 -22.68 -22.22 0.34 4.31 3.66 25376B3 ALG01 2.99 1.59 -24.58 -24.12 0.15 -1.69 -2.34 25378 cB4 ALG03 2.92 4.37 -21.06 -20.60 0.34 -1.52 -2.17 25380 cB5 ALG07 2.9 33.58 -29.44 -28.98 1.74 0.62 -0.03 25382B6 ref 1.01 44.94 -25.00 -24.54 2.59 3.96 3.31 25384B7 ref 0.99 42.28 -24.87 -24.41 2.37 4.33 3.68 25386B8 Lk Outlet Alg 3.04 31.43 -29.69 -29.23 1.07 0.95 0.30 25388B9 ALG06 3.09 35.57 -27.26 -26.80 1.96 2.79 2.14 25390B10 ALG02 3.05 5.52 -22.31 -21.85 0.45 4.72 4.07 25392C1 ALG04 2.98 37.90 -27.42 -26.96 1.36 1.21 0.56 25394 cC2 ALG05 3.04 31.74 -27.93 -27.47 2.40 0.73 0.08 25396C3 ref 0.99 38.46 -25.09 -24.63 2.40 4.37 3.72 25398

23.78 1.17

Reference statistics:

Sampling Site / Identifier:Sample Type:

Date:Tray ID and Sequence:

From%Stephanie%Hampton%(2010)% %%ESA%Workshop%on%Best%Practices%

Random0notes0

From%Stephanie%Hampton%

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C:\Documents and Settings\hampton\My Documents\NCEAS Distributed Graduate Seminars\[Wash Cres Lake Dec 15 Dont_Use.xls]Sheet1Stable Isotope Data Sheet

Wash Cresc Lake Peter's lab Don't use - old dataAlgal Washed RocksDec. 16Tray 004

SD for delta 13C = 0.07 SD for delta 15N = 0.15

Position SampleID Weight (mg) %C delta 13C delta 13C_ca %N delta 15N delta 15N_ca Spec. No.A1 ref 0.98 38.27 -25.05 -24.59 1.96 4.12 3.47 25354A2 ref 0.98 39.78 -25.00 -24.54 2.03 4.01 3.36 25356A3 ref 0.98 40.37 -24.99 -24.53 2.04 4.09 3.44 25358A4 ref 1.01 42.23 -25.06 -24.60 2.17 4.20 3.55 25360 Shore Avg ConA5 ALG01 3.05 1.88 -24.34 -23.88 0.17 -1.65 -2.30 25362 c -1.26 -27.22A6 Lk Outlet Alg 3.06 31.55 -30.17 -29.71 0.92 0.87 0.22 25364 1.26 0.32A7 ALG03 2.91 6.85 -21.11 -20.65 0.48 -0.97 -1.62 25366 cA8 ALG05 2.91 35.56 -28.05 -27.59 2.30 0.59 -0.06 25368A9 ALG07 3.04 33.49 -29.56 -29.10 1.68 0.79 0.14 25370A10 ALG06 2.95 41.17 -27.32 -26.86 1.97 2.71 2.06 25372B1 ALG04 3.01 43.74 -27.50 -27.04 1.36 0.99 0.34 25374 cB2 ALG02 3 4.51 -22.68 -22.22 0.34 4.31 3.66 25376B3 ALG01 2.99 1.59 -24.58 -24.12 0.15 -1.69 -2.34 25378 cB4 ALG03 2.92 4.37 -21.06 -20.60 0.34 -1.52 -2.17 25380 cB5 ALG07 2.9 33.58 -29.44 -28.98 1.74 0.62 -0.03 25382B6 ref 1.01 44.94 -25.00 -24.54 2.59 3.96 3.31 25384B7 ref 0.99 42.28 -24.87 -24.41 2.37 4.33 3.68 25386B8 Lk Outlet Alg 3.04 31.43 -29.69 -29.23 1.07 0.95 0.30 25388B9 ALG06 3.09 35.57 -27.26 -26.80 1.96 2.79 2.14 25390B10 ALG02 3.05 5.52 -22.31 -21.85 0.45 4.72 4.07 25392C1 ALG04 2.98 37.90 -27.42 -26.96 1.36 1.21 0.56 25394 cC2 ALG05 3.04 31.74 -27.93 -27.47 2.40 0.73 0.08 25396C3 ref 0.99 38.46 -25.09 -24.63 2.40 4.37 3.72 25398

23.78 1.17

Reference statistics:

Sampling Site / Identifier:Sample Type:

Date:Tray ID and Sequence:

From%Stephanie%Hampton%(2010)% %%ESA%Workshop%on%Best%Practices%

Wash&Cres&Lake&Dec&15&Dont_Use.xls&

From%Stephanie%Hampton%

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C:\Documents and Settings\hampton\My Documents\NCEAS Distributed Graduate Seminars\[Wash Cres Lake Dec 15 Dont_Use.xls]Sheet1Stable Isotope Data Sheet

Wash Cresc Lake Peter's lab Don't use - old dataAlgal Washed RocksDec. 16Tray 004

SD for delta 13C = 0.07 SD for delta 15N = 0.15

Position SampleID Weight (mg) %C delta 13C delta 13C_ca %N delta 15N delta 15N_ca Spec. No.A1 ref 0.98 38.27 -25.05 -24.59 1.96 4.12 3.47 25354A2 ref 0.98 39.78 -25.00 -24.54 2.03 4.01 3.36 25356A3 ref 0.98 40.37 -24.99 -24.53 2.04 4.09 3.44 25358A4 ref 1.01 42.23 -25.06 -24.60 2.17 4.20 3.55 25360 Shore Avg ConA5 ALG01 3.05 1.88 -24.34 -23.88 0.17 -1.65 -2.30 25362 c -1.26 -27.22A6 Lk Outlet Alg 3.06 31.55 -30.17 -29.71 0.92 0.87 0.22 25364 1.26 0.32A7 ALG03 2.91 6.85 -21.11 -20.65 0.48 -0.97 -1.62 25366 cA8 ALG05 2.91 35.56 -28.05 -27.59 2.30 0.59 -0.06 25368A9 ALG07 3.04 33.49 -29.56 -29.10 1.68 0.79 0.14 25370A10 ALG06 2.95 41.17 -27.32 -26.86 1.97 2.71 2.06 25372B1 ALG04 3.01 43.74 -27.50 -27.04 1.36 0.99 0.34 25374 c SUMMARY OUTPUTB2 ALG02 3 4.51 -22.68 -22.22 0.34 4.31 3.66 25376B3 ALG01 2.99 1.59 -24.58 -24.12 0.15 -1.69 -2.34 25378 c Regression StatisticsB4 ALG03 2.92 4.37 -21.06 -20.60 0.34 -1.52 -2.17 25380 c Multiple R 0.283158B5 ALG07 2.9 33.58 -29.44 -28.98 1.74 0.62 -0.03 25382 R Square 0.080178B6 ref 1.01 44.94 -25.00 -24.54 2.59 3.96 3.31 25384 Adjusted R Square-0.022024B7 ref 0.99 42.28 -24.87 -24.41 2.37 4.33 3.68 25386 Standard Error1.906378B8 Lk Outlet Alg 3.04 31.43 -29.69 -29.23 1.07 0.95 0.30 25388 Observations 11B9 ALG06 3.09 35.57 -27.26 -26.80 1.96 2.79 2.14 25390B10 ALG02 3.05 5.52 -22.31 -21.85 0.45 4.72 4.07 25392 ANOVAC1 ALG04 2.98 37.90 -27.42 -26.96 1.36 1.21 0.56 25394 c df SS MS F Significance FC2 ALG05 3.04 31.74 -27.93 -27.47 2.40 0.73 0.08 25396 Regression 1 2.851116 2.851116 0.784507 0.398813C3 ref 0.99 38.46 -25.09 -24.63 2.40 4.37 3.72 25398 Residual 9 32.7085 3.634278

23.78 1.17 Total 10 35.55962

CoefficientsStandard Error t Stat P-value Lower 95%Upper 95%Lower 95.0%Upper 95.0%Intercept -4.297428 4.671099 -0.920003 0.381568 -14.8642 6.269341 -14.8642 6.269341X Variable 1-0.158022 0.17841 -0.885724 0.398813 -0.561612 0.245569 -0.561612 0.245569

Reference statistics:

Sampling Site / Identifier:Sample Type:

Date:Tray ID and Sequence:

Random0stats0output0

From%Stephanie%Hampton%

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C:\Documents and Settings\hampton\My Documents\NCEAS Distributed Graduate Seminars\[Wash Cres Lake Dec 15 Dont_Use.xls]Sheet1Stable Isotope Data Sheet

Wash Cresc Lake Peter's lab Don't use - old dataAlgal Washed RocksDec. 16Tray 004

SD for delta 13C = 0.07 SD for delta 15N = 0.15

Position SampleID Weight (mg) %C delta 13C delta 13C_ca %N delta 15N delta 15N_ca Spec. No.A1 ref 0.98 38.27 -25.05 -24.59 1.96 4.12 3.47 25354A2 ref 0.98 39.78 -25.00 -24.54 2.03 4.01 3.36 25356A3 ref 0.98 40.37 -24.99 -24.53 2.04 4.09 3.44 25358A4 ref 1.01 42.23 -25.06 -24.60 2.17 4.20 3.55 25360 Shore Avg ConA5 ALG01 3.05 1.88 -24.34 -23.88 0.17 -1.65 -2.30 25362 c -1.26 -27.22A6 Lk Outlet Alg 3.06 31.55 -30.17 -29.71 0.92 0.87 0.22 25364 1.26 0.32A7 ALG03 2.91 6.85 -21.11 -20.65 0.48 -0.97 -1.62 25366 cA8 ALG05 2.91 35.56 -28.05 -27.59 2.30 0.59 -0.06 25368A9 ALG07 3.04 33.49 -29.56 -29.10 1.68 0.79 0.14 25370A10 ALG06 2.95 41.17 -27.32 -26.86 1.97 2.71 2.06 25372B1 ALG04 3.01 43.74 -27.50 -27.04 1.36 0.99 0.34 25374 c SUMMARY OUTPUTB2 ALG02 3 4.51 -22.68 -22.22 0.34 4.31 3.66 25376B3 ALG01 2.99 1.59 -24.58 -24.12 0.15 -1.69 -2.34 25378 c Regression StatisticsB4 ALG03 2.92 4.37 -21.06 -20.60 0.34 -1.52 -2.17 25380 c Multiple R 0.283158B5 ALG07 2.9 33.58 -29.44 -28.98 1.74 0.62 -0.03 25382 R Square 0.080178B6 ref 1.01 44.94 -25.00 -24.54 2.59 3.96 3.31 25384 Adjusted R Square-0.022024B7 ref 0.99 42.28 -24.87 -24.41 2.37 4.33 3.68 25386 Standard Error1.906378B8 Lk Outlet Alg 3.04 31.43 -29.69 -29.23 1.07 0.95 0.30 25388 Observations 11B9 ALG06 3.09 35.57 -27.26 -26.80 1.96 2.79 2.14 25390B10 ALG02 3.05 5.52 -22.31 -21.85 0.45 4.72 4.07 25392 ANOVAC1 ALG04 2.98 37.90 -27.42 -26.96 1.36 1.21 0.56 25394 c df SS MS F Significance FC2 ALG05 3.04 31.74 -27.93 -27.47 2.40 0.73 0.08 25396 Regression 1 2.851116 2.851116 0.784507 0.398813C3 ref 0.99 38.46 -25.09 -24.63 2.40 4.37 3.72 25398 Residual 9 32.7085 3.634278

23.78 1.17 Total 10 35.55962

CoefficientsStandard Error t Stat P-value Lower 95%Upper 95%Lower 95.0%Upper 95.0%Intercept -4.297428 4.671099 -0.920003 0.381568 -14.8642 6.269341 -14.8642 6.269341X Variable 1-0.158022 0.17841 -0.885724 0.398813 -0.561612 0.245569 -0.561612 0.245569

Reference statistics:

Sampling Site / Identifier:Sample Type:

Date:Tray ID and Sequence:

SampleID ALG03 ALG05 ALG07 ALG06 ALG04 ALG02 ALG01 ALG03 ALG07

Weight (mg) 2.91 2.91 3.04 2.95 3.01 3 2.99 2.92 2.9

%C 6.85 35.56 33.49 41.17 43.74 4.51 1.59 4.37 33.58delta 13C -21.11 -28.05 -29.56 -27.32 -27.50 -22.68 -24.58 -21.06 -29.44

delta 13C_ca -20.65 -27.59 -29.10 -26.86 -27.04 -22.22 -24.12 -20.60 -28.98

%N 0.48 2.30 1.68 1.97 1.36 0.34 0.15 0.34 1.74delta 15N -0.97 0.59 0.79 2.71 0.99 4.31 -1.69 -1.52 0.62

delta 15N_ca -1.62 -0.06 0.14 2.06 0.34 3.66 -2.34 -2.17 -0.03

-3.00

-2.00

-1.00

0.00

1.00

2.00

3.00

4.00

-35.00 -30.00 -25.00 -20.00 -15.00 -10.00 -5.00 0.00

Series1

From%Stephanie%Hampton%

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UGLY TRUTH

Data&management?&

Metadata?&

Data&repositories?&

Share&data&publicly?&

Why&share&data?&

&

From

%Flickr%by%s%i%b%e%r%

ABOUT RESEARCHERS

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From

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n327%

Who0cares?0

From%Flickr%by%ReddenTMcAllister%

From%Flickr%by%AJC1%

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From%Flickr%by%Michael%Tinkler%

?0

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From%Flickr%by%iowa_spirit_walker%

•  Cost&•  Confusion&about&standards&

•  Lack&of&training&•  Fear&of&lost&rights&or&benefits&

•  No&incentives&

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From

%Flickr%by%thew

ma1

%

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Intercept&researchers&where&they&already0work0

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Facilitate&

Archiving0

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Publishing0

Data&management&&&organization&

Data&Reuse&&&Reproducibility&

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What0do0scientists0need0help0with?0

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Asked&~2000scientists&What&does&your&data&look&like?&

How&do&you&capture&metadata?&

Plans&for&saving&&&sharing&data?&

Repositories?&

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What0the0tool0should0do:00

Best&practices&check&Generate&metadata&(EML)&Get&identifier&+&citation&Post&data&to&repository&&

From%Flickr%by%Rennett%Stowe%

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dataup.cdlib.org0

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Addain&and&web&application&

?

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AddQin&&•  Software&you&download&&&install&•  Appears&as&“ribbon”&in&Excel&•  Works&for&Windows&Excel&2007+&

WebQbased0application&&•  Upload&file&to&website&•  Works&for&any&platform&•  But…&new&user&interface&

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DataUp00Features0&Best&practices&check&Generate&metadata&Get&identifier&&&citation&Post&data&to&repository&

From%Flickr%by%SoulRider.222%

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Best&Practices&Check&

•  Embedded&charts,&tables,&pictures&

•  Embedded&comments&

•  Commas&•  Special&

characters&•  Coloracoded&text&

&&cell&shading&•  Columns&with&

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From%Flickr%by%ex.libris%

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DataUp00Features0&Best&practices&check&Generate&metadata&Get&identifier&&&citation&Post&data&to&repository&

From%Flickr%by%SoulRider.222%

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•  Digital0context0

•  Name&of&the&data&set&

•  The&name(s)&of&the&data&file(s)&in&the&data&set&

•  Date&the&data&set&was&last&modified&

•  Example&data&file&records&for&each&data&type&file&

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•  List&of&related&or&ancillary&data&sets&

•  Software&(including&version&number)&used&to&prepare/read&&the&data&set&

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•  Where&collected&&&spatial&resolution&When&collected&&&temporal&resolution&

•  Standards&or&calibrations&used&

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•  Information0about0data0

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Allows&readers&to&find&data&products&Get&credit&for&data&and&publications&

Promotes&reproducibility&Better&measure&of&research&impact&

Example:0Sidlauskas,&B.&2007.&Data&from:&Testing&for&unequal&rates&of&morphological&diversification&in&the&absence&of&a&detailed&phylogeny:&a&case&study&from&characiform&fishes.&Dryad&Digital&Repository.&doi:10.5061/dryad.20&

From%Flickr%by%maybeemily%

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DataUp00Features0&Best&practices&check&Generate&metadata&Get&identifier&&&citation&Post&data&to&repository&

From%Flickr%by%SoulRider.222%

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Data&Repository&for0

Anyone0|0Anywhere0

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DataUp&Web&App&

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Web0App0

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Web0App0

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Web0App:0Best0Practices0Check0

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Web0App:0Metadata0

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Web0App:0Citation0

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Web0App:0Posting0to0repository0

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Web0App:0Posting0to0repository0

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DataUp&AddaIn&

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AddQin:0Ribbon0

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AddQin:0Metadata0tab0

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AddQIn0•  Windows&PC&2007+&•  No&logain&required&•  Offline&&&online&•  Can&view&metadata&via&

tab&•  See&check&alongside&

data&•  Select&header&row&

Web0app0•  Any&platform&•  Logain&required&•  Online&only&•  Can’t&view&metadata&

once&generated&•  Get&locations&for&check&

•  Manual&header&row&entry&

VS0

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Main0site:0dataup.cdlib.org0

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•  New&language&

•  Focus&on&web&app&

•  Emphasize&Best&Practices&Check&

•  Leverage&existing&tools&

•  Enable&Customization&

From%animationresources.org%

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dataup.cdlib.org&bitbucket.org/dataup/main&

Website&Code&site&

My&website&Email&me&Tweet&me&My&slides&CDL&Blog&

carlystrasser.net&[email protected]&@carlystrasser&&slideshare.net/carlystrasser&datapub.cdlib.org&