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====2/8/2017 WEDNESDAY Id Id2 Geography Total; Estimate; Population 25 years and over Total; Estimate; Population 25 years and over - High school graduate (includes equivalency) Total; Margin of Error; Population 25 years and over - High school graduate (includes equivalency) Total; Margin of Error; Population 25 years and over - High school graduate (includes equivalency) Percent; Margin of Error; Population 25 years and over - High school graduate (includes equivalency) Total; Estimate; Population 25 years and over - Associate's degree Total; Margin of Error; Population 25 years and over - Associate'9AMs degree Percent; Estimate; Population 25 years and over -11AMAssociate's degree Percent; Margin of Error; Population 25 years and over - Associate'==== s degree* Attempted to come up with possible cases for locating the description Total; Estimate; Population 25 years and over - Bachelor's degree Total; Margin of Error; Population 25 years and over - Bachelor's degree Percent; Estimate; Population 25 years and over - Bachelor's degree Percent; Margin of Error; Population 25 years and over - Bachelor's degree Total; Estimate; Population 25 years and over - Graduate or professional degree Total; Margin of Error; Population 25 years and over - Graduate or professional degree Percent; Estimate; Population 25 years and over - Graduate or professional degree Percent; Margin of accelerators Error; Population 25 years and over - pick up from extracting bodies Graduate or professional degree Percent; Estimate; Percent high school graduate or higher Percent; Margin of text from the about page (given that it exists)Error; Percent high school graduate or higher Percent; Estimate; Percent bachelor's degree or higher Percent; Margin of Error; Percent bachelor's degree or higher
====2/13/2017 MONDAY *Complications:**For csv files corresponding to years 2015 & 2016, all of the above columns exist.**For csv files corresponding to years 2005 - 2014, no 'Percent'2PM-6PMcolumns exist*** Instead their 'Total'====columns are percentage values* Goals (for trials): 1) Build ER Diagram 2) *For each entitycsv file corresponding to year 2005, get XML snippet 3) Build a parser/ripper for single file; the python parser can be found at: E:\McNair\Projects\FDA Trials\Jeemin_Projectcolumns regarding Graduate or professional degree are labeled differently.* [[Trial Data Project]]*2012 data doesn't correspond to Population 25 years and over.
====2/15/2017 WEDNESDAY ''9AM-11AM''====*Temporary Solution:* Discussed with Catherine what to do with FDA Trial data and decided *Since the above problems may be specific to have a dictionary with zip-codes as keys and number this set of trials occurred in that zipcode as values. Was still attempting to loop tables, will go through the csv files without the code having to exist in the same directory as the XML files. Plan to write to excel via tsv, with zip-code as one column and # of occurrence as the otheradjust columns.
====2/17/2017 FRIDAY ''2PM-6PM''====* Completed code for counting the number of occurrences for each unique zipcode. (currently titled & located: E:\McNair\Projects\FDA Trials\Jeemin_Project\Jeemin_Running_File.py). It has been running for 20+min because of the comprehensive XML data files. Meanwhile started coding to create a dictionary with the keys corresponding to each unique trial ID, mapped to every other information (Python script location, sponsors, phase, drugs ...etc.) (currently titled & located: E:\McNair\Projects\FDA TrialsAgglomeration\Jeemin_ProjectACS_Downloaded_Data\Jeemin_FDATrial_as_key_data_rippingpullCertainColumns.py).
====2/20/2017 MONDAY ''2PM-410-31:30PM''====* Continued working on Jeemin_FDATrial_as_key_data_rippingFinished doanloading files from ACS.* Started loading tables into tigertest.py to find tags and place all of those information * Commands run could be found in a list. The other zipcode file did not finish executing after 2+ hours of running it - considering the possibility of splitting the record file into smaller bits, or running the processing on a faster machine E:\McNair\Projects\Agglomeration\ACS_Downloaded_Data\DataLoading_SQL_Commands.txt
====2/22/2017 WEDNESDAY ''9AM-1210-30:30PM''====* Finished Jeemin_FDATrial_as_key_data_ripping.py (E:\McNair\Projects\FDA Trials\Jeemin_Project\Jeemin_FDATrial_as_key_data_ripping.py)Downloaded data from ACS, which outputs to be continued* File path: E:\McNair\Projects\FDA TrialsAgglomeration\Jeemin_Project\general_data_ripping_output.txt; TODOACS_Downloaded_Data* Fields of interest: output four different tables & replace the write in the same for S1401 SCHOOL ENROLLMENT S1501 EDUCATIONAL ATTAINMENT S2301 EMPLOYMENT STATUS B01003 TOTAL POPULATION B02001 RACE B07201 GEOGRAPHICAL MOBILITY B08303 TRAVEL TIME TO WORK B19013 MEDIAN HOUSEHOLD INCOME B19053 SELF-loop as going through each fileEMPLOYMENT INCOME IN THE PAST 12 MONTHS FOR HOUSEHOLDS B19083 GINI INDEX OF INCOME INEQUALITY B25003 TENURE B25105 MEDIAN MONTHLY HOUSING COSTS B28011 INTERNET SUBSCRIPTIONS IN HOUSEHOLD G001 GEOGRAPHIC IDENTIFIERS
====2/24/2017 FRIDAY ''2:30PM-610-23:30PM''====* Continued working on producing multiple tables - first two are doneTalked to Ed with Peter & Oliver about upcoming tasks & projects. Was working * Loaded acs_place table 2017 (does not contain population) on location, as there are multiple location tags per locationtigertest.** SQL commands used:
====2/27/2017 MONDAY ''2PM-6PM''====* Finished producing tables from Jeemin_FDATrial_as_key_data_ripping.py* Talked to Julia about LinkedIn data extracting - to be discussed further with Julia & Peter.* Started web crawler for Wikipedia - currently pulls Endowment, Academic staff, students, undergraduates, and postgraduates info found on Rice Wikipedia page. Can be found in : E:\McNair\Projects\University Patents\Jeemin_University_wikipedia_crawler.py DROP TABLE acs_place;
====3/1/2017 WEDNESDAY ''9AM-12PM''==== CREATE TABLE acs_place (* Started re-running Jeemin_FDATrial_as_key_data_ripping.py USPS varchar(5), GEOID varchar(30), ANSICODE varchar(30), NAME varchar(100), LSAD varchar(30), FUNCSTAT varchar(10), ALAND varchar(30), AWATER varchar(30), ALAND_SQMI varchar(30), AWATER_SQMI varchar(30), INTPTLAT varchar(30), INTPTLONG varchar(30) );
====3 \COPY acs_place FROM '/3bulk/2017 FRIDAY 2017_Gaz_place_national.txt''2PM; --5PM''====* Attempted to output sql tablesCOPY 29578
====3/6/017 MONDAY ''2PM-6PM''====* TODO:* [[Installing python in a database]]* Find acs place 2016 data for population* Added building Python function section to [[Working with PostgreSQL]] at the bottom of the page.* Ran FDA Trial data ripping againFind larger acs files, as ideally at the text output files were wiped. place level* Plan on discussing with Julia and Meghana again about pulling universities and other relevant institutions from the Assignee List USA. * Talked to Sonia about pulling city, state, zipcode information, hence python was installed in a database. Will work with Sonia Provide more documentation on Wednesday afternoon and see how best a regex function could be implementedPOSTGIS & geocoding
====3/8/2017 WEDNESDAY ''9AM-12PM''====10-16:* Output sql tables Exported maps of points from finished run of Jeemin_FDATrial_as_key_data_rippingthe Bay Area each year.py * Ran through assigneelist_USA.txt to see how many different ways UNIVERSITY could be spelled wrong. There were many* Map used location: E:\McNair\Projects\Agglomeration\HarrisonPeterWorkArcGIS\Jeemin_Bay_Area Points_Every_Year\BayAreaEveryYearMap** Zoom scale: 1:650.000* Tried to logic through creating a pattern that could catch all different versions Location of UNIVERSITY. Discuss further on whether UNIVERSITIES and those that include UNIVERSITIES but include Bay Area Points png files: INC in the end should be pulled as relevant informationE:\McNair\Projects\Agglomeration\HarrisonPeterWorkArcGIS\Jeemin_Bay_Area Points_Every_Year
====32017-10-10:*Discoveries/ Struggles regarding.gdb to .shp file conversion:** Esri Production Mapping (costly)*** License needs to be purchasesd: http://8www.esri.com/2017 WEDNESDAY ''2PMsoftware/arcgis/extensions/production-5PM ''====mapping/pricing* Wrote regex pattern that identifies all "university" matchings * Use ogr2ogr from gdal package*** https://gis.stackexchange.com/questions/14432/migrating-geodatabase-data-into-postgis-without-esri- can be found in Eapps*** Command:\McNair\Projects\University Patents\university_pulled_from_assignee_list_USA ogr2ogr -- is an output f "ESRI Shapefile" [Destination of shapefile] [path to gdb file]* Talked to Sonia, but didn't come to solid conclusion on identifying whether key words associate with city or country by running a python function** Problem installing gdal
====3/13/2017 MONDAY ''12PM-2PM10-09:* TODO''====S:** Downloading data onto tigertest*** Road*** Railway*** Coastline* For University Patent Data Matching - matched SCHOOL (output** Instructions: Ehttp:\McNair\Projects\University Patents\school_pulled_from_assignee_list_USA//www.edegan.com/wiki/PostGIS_Installation#Bulk_Download_TIGER_Shapefiles** Configure census data from American Community Survey (ACS)*** 1) and matched INSTITUTEWork out what data is of our interest (outputconfirm ACS)*** 2) Determine appropriate shape file unit: E:\McNair\Projects\University Patents\institute_pulled_from_assignee_list_USA)**** census block vs. census block group vs. census track* [[University Patent Matching]] * To be worked on later: Grant XML parsing & general name matcher* 3) Load into tigertest
====3* Done:** Downloaded data from https://www.census.gov/cgi-bin/14geo/2017 TUESDAY ''12PMshapefiles/index.php tl_2017_us_coastline -- 4209 tl_2017_us_primaryroads -- 11574 tl_2017_us_rails -2PM''====- 176237* Started pulling academy cases but there are too many cases * Link found to worry about, in terms of institution of interestpotentially download ACS data: https://www. A document is located in E:\McNair\Projects\University Patents\academies_verify_casescensus.txt* Need Juliagov/geo/maps-data/data/Meghana to look through the hits and see which are relevant & extract pattern from theretiger-data. html* Having trouble outputting txt file without double quotes around every line. * Thinking that one text file should be output for all keywords instead of having one each, to avoid overlap (ex) COLLEGE and UNIVERSITY are both keywords; ALBERT EINSTEIN COLLEGE OF YESHIVA UNIVERSITY will be hit twice if * But most files on it were counted as two separate instances, one accounting for COLLEGE come with .gdb extension and the other for UNIVERSITY) - either in the form of if-elseif statements or one big regex checknot .shp
====3/15/2017 WEDNESDAY ''9AM-1PM''====10-03:* Todo: write a wikipage Installed PostGIS & is now visible on possible input/output info on string matcher* Wrote part of XML parser, extracted yearly data into E:\McNair\Projects\Federal Grant Data\NSF\NSF Extracted Data (up to year 2010)pgAdmin III
====* ArcGIS (connect to postgis database):** 1) Open ArcMap** 2) Either open blank or open existing file/project** 3/16/2017 THURSDAY ) Click on 'Add Data'12PMbutton with a cross and a yellow diamond (under Selection toolbar)** 4) Go to the top-2PMmost directory by pressing on the arrow that points left-then-up (on the left of home button)** 5) Click on 'Database Connections'** 6) Click on 'Add Database Connection'====(if Connection to localhost.sde) does not exist already)** 7) Fill in the following fields:*** Database Platform: PostgreSQL*** Instance: localhost* Further documented [[University Patent Matching]]** User name: postgres* Finished writing XML Parser** Password: *** Database: tigertest** 8) Press 'OK'** 9) Now you'll have 'Connection to localhost.sde' in your Database Connections** 10) Double click on 'Connection to localhost.sde'** 11) Double click on the table of interest** 12) Click 'Finish'** 13) You'll see information populated on map, as one of the 'Layers'*** Tested with: tigertest.public.copointplacescontains
====3/20/2017 MONDAY * On running & altering Oliver''2PMs script: ** Location: E:\McNair\Projects\OliverLovesCircles\src\python\vc_circles.py** Ed manipulated file names so that underscores would replace dots (St.Louis --6PM''====> St_Louis)* Talked to Julia about universal matcher, want to combine all University * Takes in instances and sweep times as part of California's to University of Californiathe argument, The Regents ofbut not impactful as those variables are hardcoded in the script* Converted crunchbase2013 data from mySQL to PostgreSQL, but having trouble * Ran vc_circles.py with the last table - cb_relationships, complains about syntax error at or near some places - but generally all tables exist in database called crunchbasefollowing variables with changed values:*** SWEEP_CYCLE_SECONDS = 10 (used to be 30)*** NUMBER_INSTANCES = 16 (used to be 8)* Federal Grant Data XML Parser was run - the three * New output textfiles can to be found in : E:\McNair\Projects\Federal Grant DataOliverLovesCircles\NSFout
====3/22/2017 WEDNESDAY ''9AM-12PM10-02:* Talked to Harrison & Peter regarding ArcGIS** Currently have points plotted on Houston** Trouble interpreting geometry type, as currently reads in from text file** Documents located in : E:\McNair\Projects\Agglomeration\HarrisonPeterWorkArcGIS* Attempted to install PostGIS spatial extention from PostgreSQL but getting 'spatial database creation failed'====error message.* Read string matching & calculating distance, below are relevant links* Referenced instructions: * [http** https://www.cs.cmugpsfiledepot.educom/~wcohentutorials/postscript/ijcaiinstalling-and-setting-up-postgresql-wswith-2003.pdf]postgis/* [http://web.archive.org/web/20081224234350/** http://www.dcsbostongis.shef.ac.ukcom/~sam/stringmetricsPrinterFriendly.html]aspx?content_name=postgis_tut01
====3/24/2017 FRIDAY ''2PM-5PM''====09-26:* Discussed with Julia & Meghana about university keys Created a table that maps a state to use to count the database name.** http://www.edegan.com/wiki/PostGIS_Installation# of occurrencesTranslating_Table_names_to_corresponding_States* Added more GIS-information (functions, including aliases and misspellingsrealm & outliers to consider)* Thoughts* http: to use a scoring metric with a key of UNIVERSITY OF CALIFORNIA SYSTEM, it should have a 'better' score when compared to MATHEMATICAL SCIENCES PUBLISHERS C/O UNIVERSITY OF CALIFORNIA BERKELEY or CALIFORNIA AT LOS ANGELES, UNVIERSITY OF than when compared to UNIVERSITY OF SOUTHERN CALIFORNIA, which may pose a challenge when attempting to implement this in a more general sense/www. In normalizing a string, strip "THE", "," and split words by spaces and compare each keyword from the two stringsedegan. Deciding on which strings com/wiki/Urban_Start-up_Agglomeration#GIS_Resources* Visualization in PostGIS or connecting to compare will be another issue - length ArcGIS for visualization (within some range maybeimport/export data) could be an option. * Federal Grant Data XML Parser was rerun - same output textfilesSpatial indexing:** http://revenant.ca/www/postgis/workshop/indexing.html
====3/27/2017 MONDAY ''2PM-6PM''====09-25:* Writing code for university matches - decided Talked to go through keys instead Ed about GIS, Census data, and going about determining the correctness of reported 'place.' Currently script makes a cross product of each dataitemreported place and an existing place, outputting a column of boolean value to indicate whether the reported place's coordinates fell within a place's geometric boundaries. Use keywords in each key One other way of going about this which we discussed is to first check if the reported place does fall within that place's boundaries. If it isn't, we'll go through about the dataitem - misspellings are currently unaccounted forcross product method.
====3* To add documentation : ** http:/29/2017 WEDNESDAY''2PM-5PM''====* Troubled by the variety of cases - separating keys by keywords will not work favorably when it hits University of California vswww. University of Southern California case - find a way to match University of Southern California first (more specific ones first) - but how to generalizeedegan...====4com/12wiki/2017 WEDNESDAY''9AM-12PM''====PostGIS_Installation* Finishing up cleaning the columns for Federal Grant Data - NIH. The output excel files can be accessed at* http: E:\McNair\Projects\Federal Grant Data\NIH\Grants Titled: Jeemin_combined_files 1986-2001//www.csv Jeemin_combined_files 2002-2012edegan.csv Jeemin_combined_files 2013com/wiki/Urban_Start-2015.csvup_Agglomeration
CREATE TABLE all_grants (*Relevant File paths: APPLICATION_ID integer,**E:\McNair\Projects\Agglomeration\TestGIS.sql ACTIVITY varchar(3),**Z:\VentureCapitalData\SDCVCData\vcdb2\ProecssingCoLevelSimple.sql ADMINISTERING_IC varchar(2), APPLICATION_TYPE varchar(1), ARRA_FUNDED varchar(1), AWARD_NOTICE_DATE date, BUDGET_START date, BUDGET_END date, CFDA_CODE varchar(3), CORE_PROJECT_NUM varchar(11), ED_INST_TYPE varchar(30), FOA_NUMBER varchar(13), FULL_PROJECT_NUM varchar(35), FUNDING_ICs varchar(40), FUNDING_MECHANISM varchar(23), FY smallint, IC_NAME varchar(77), NIH_SPENDING_CATS varchar(295), ORG_CITY varchar(20), ORG_COUNTRY varchar(16), ORG_DEPT varchar(30), ORG_DISTRICT smallint, ORG_DUNS integer, ORG_FIPS varchar(2), ORG_NAME varchar(60), ORG_STATE varchar(2), ORG_ZIPCODE integer, PHR varchar(200), PI_IDS varchar(30), PI_NAMEs varchar(200), PROGRAM_OFFICER_NAME varchar(36), PROJECT_START date, PROJECT_END date, PROJECT_TERMS varchar(200), PROJECT_TITLE varchar(244), SERIAL_NUMBER smallint, STUDY_SECTION varchar(4), STUDY_SECTION_NAME varchar(100), SUBPROJECT_ID smallint, SUFFIX varchar(2), SUPPORT_YEAR smallint, DIRECT_COST_AMT integer, INDIRECT_COST_AMT integer, TOTAL_COST integer, TOTAL_COST_SUB_PROJECT integer ); **Z:\VentureCapitalData\SDCVCData\vcdb2\COPY all_grants FROM 'Jeemin_combined_files 1986-2001CitiesWithGT10Active.csv' WITH DELIMITER AS E'\t' HEADER NULL AS ''CSVtxt
====4/14/2017 FRIDAY-09-21:* Functions for Linear Referencing: '''ST_LineInterpolatePoint(geometry A, double measure)''': Returns a point interpolated along a line. '''ST_LineLocatePoint(geometry A, geometry B)''2PM-5PM': Returns a float between 0 and 1 representing the location of the closest point on LineString to the given Point. '''ST_Line_Substring(geometry A, double from, double to)''': Return a linestring being a substring of the input one starting and ending at the given fractions of total 2d length. '''ST_Locate_Along_Measure(geometry A, double measure)''': Return a derived geometry collection value with elements that match the specified measure. '''ST_Locate_Between_Measures(geometry A, double from, double to)'''====: Return a derived geometry collection value with elements that match the specified range of measures inclusively.* Loaded Federal Grants Data into database '''ST_AddMeasure(geometry A, double from, double to)''': Return a derived geometry with measure elements linearly interpolated between the start and end points. If the geometry has no measure dimension, one is added.
====4/17/2017 MONDAY*3-D Functions: '''ST_3DClosestPoint''' — Returns the 3-dimensional point on g1 that is closest to g2. This is the first point of the 3D shortest line. '''ST_3DDistance''' — For geometry type Returns the 3-dimensional cartesian minimum distance (based on spatial ref) between two geometries in projected units. '''ST_3DDWithin''' — For 3d (z) geometry type Returns true if two geometries 3d distance is within number of units. '''ST_3DDFullyWithin''' — Returns true if all of the 3D geometries are within the specified distance of one another. '''2PMST_3DIntersects''' — Returns TRUE if the Geometries “spatially intersect” in 3d -4PMonly for points and linestrings ''===='ST_3DLongestLine''' — Returns the 3-dimensional longest line between two geometries '''ST_3DMaxDistance''' — For geometry type Returns the 3-dimensional cartesian maximum distance (based on spatial ref) between two geometries in projected units. '''ST_3DShortestLine''' — Returns the 3-dimensional shortest line between two geometries
====4/17/2017 WEDNESDAY''9AM-12PM''====* To pull acceleratorsRelevant PostgreSQL Commands: Wrote simple python regex-based script that ran on organizations data. Code: E:'''\McNair\Projects\Accelerators\Crunchbase Snapshot\accelerator keywordsdt *.py*''' Show all tables Matched output (885 mathces) : E:'''\McNair\Projects\Accelerators\Crunchbase Snapshot\Jeemin_885_accel_matchesq''' Exit table
====9*Specifities/11/2017 MONDAY''4PM-6PM''====Outliers to consider: New York (decompose) Princeton area (keep Princeton unique) Reston, Virginia (keep) San Diego (include La Jolla)* Ensured that documentation exists for the projects worked on last semester. Silicon Valley (all distinct)
====9* Continue reading from: https:/12/2017 TUESDAY''9AM-10:40AM & 1PM-2:20PM & 4PM-5:30PM''====* Clarified University Matching output filepostgis.* Helped Christy with pdf-reader, capturing keywords in readable formatnet/docs/postgis_installation.html
..2017-09-20:* Attended first intro to GIS course yesterday* Updated above notes on GIS
====9/18/2017 MONDAY''4PM-6PM''====
* Read documentation on PostGIS and tiger geocoder
* Continue reading from: http://workshops.boundlessgeo.com/postgis-intro/joins.html
====9/19/2017 TUESDAY''9AM-10:40AM & 1PM09-219:20PM''====
====9/20/2017 WEDNESDAY''3:50PM-5:20PM''====
* Attended first intro to GIS course yesterday
* Updated above notes on GIS
* Continue reading from:
====92017-09-18:* Read documentation on PostGIS and tiger geocoder* Continue reading from: http://workshops.boundlessgeo.com/21postgis-intro/joins.html 2017 THURSDAY''9AM-09-12:30PM''====* Functions for Linear Referencing:Clarified University Matching output file. '''ST_LineInterpolatePoint(geometry A* Helped Christy with pdf-reader, double measure)''': Returns a point interpolated along a linecapturing keywords in readable format. '''ST_LineLocatePoint(geometry A, geometry B)'''2017-09-11: Returns a float between 0 and 1 representing * Ensured that documentation exists for the location of the closest point projects worked on LineString to the given Pointlast semester. '''ST_Line_Substring(geometry A, double from, double to)'''</onlyinclude> ===Spring 2017=== 2017-04-17: Return a linestring being a substring of the input one starting and ending at the given fractions of total 2d length. '''ST_Locate_Along_Measure(geometry A, double measure)'''* To pull accelerators: Return a derived geometry collection value with elements Wrote simple python regex-based script that match the specified measureran on organizations data. '''ST_Locate_Between_Measures(geometry A, double from, double to)'''Code: E: Return a derived geometry collection value with elements that match the specified range of measures inclusively\McNair\Projects\Accelerators\Crunchbase Snapshot\accelerator keywords.py '''ST_AddMeasureMatched output (geometry A, double from, double to885 mathces)''': Return a derived geometry with measure elements linearly interpolated between the start and end points. If the geometry has no measure dimension, one is added.E:\McNair\Projects\Accelerators\Crunchbase Snapshot\Jeemin_885_accel_matches
*32017-04-D Functions14: '''ST_3DClosestPoint''' — Returns the 3-dimensional point on g1 that is closest to g2. This is the first point of the 3D shortest line. '''ST_3DDistance''' — For geometry type Returns the 3-dimensional cartesian minimum distance (based on spatial ref) between two geometries in projected units. '''ST_3DDWithin''' — For 3d (z) geometry type Returns true if two geometries 3d distance is within number of units. '''ST_3DDFullyWithin''' — Returns true if all of the 3D geometries are within the specified distance of one another. '''ST_3DIntersects''' — Returns TRUE if the Geometries “spatially intersect” in 3d - only for points and linestrings '''ST_3DLongestLine''' — Returns the 3-dimensional longest line between two geometries '''ST_3DMaxDistance''' — For geometry type Returns the 3-dimensional cartesian maximum distance (based on spatial ref) between two geometries in projected units. '''ST_3DShortestLine''' — Returns the 3-dimensional shortest line between two geometries* Loaded Federal Grants Data into database
* Continue reading from: https://postgis CREATE TABLE all_grants ( APPLICATION_ID integer, ACTIVITY varchar(3), ADMINISTERING_IC varchar(2), APPLICATION_TYPE varchar(1), ARRA_FUNDED varchar(1), AWARD_NOTICE_DATE date, BUDGET_START date, BUDGET_END date, CFDA_CODE varchar(3), CORE_PROJECT_NUM varchar(11), ED_INST_TYPE varchar(30), FOA_NUMBER varchar(13), FULL_PROJECT_NUM varchar(35), FUNDING_ICs varchar(40), FUNDING_MECHANISM varchar(23), FY smallint, IC_NAME varchar(77), NIH_SPENDING_CATS varchar(295), ORG_CITY varchar(20), ORG_COUNTRY varchar(16), ORG_DEPT varchar(30), ORG_DISTRICT smallint, ORG_DUNS integer, ORG_FIPS varchar(2), ORG_NAME varchar(60), ORG_STATE varchar(2), ORG_ZIPCODE integer, PHR varchar(200), PI_IDS varchar(30), PI_NAMEs varchar(200), PROGRAM_OFFICER_NAME varchar(36), PROJECT_START date, PROJECT_END date, PROJECT_TERMS varchar(200), PROJECT_TITLE varchar(244), SERIAL_NUMBER smallint, STUDY_SECTION varchar(4), STUDY_SECTION_NAME varchar(100), SUBPROJECT_ID smallint, SUFFIX varchar(2), SUPPORT_YEAR smallint, DIRECT_COST_AMT integer, INDIRECT_COST_AMT integer, TOTAL_COST integer, TOTAL_COST_SUB_PROJECT integer ); \COPY all_grants FROM 'Jeemin_combined_files 1986-2001.net/docs/postgis_installation.htmlcsv' WITH DELIMITER AS E'\t' HEADER NULL AS ''CSV
====9/25/2017 MONDAY''4PM-6PM''====03-29:* Talked to Ed about GIS, Census data, and going about determining Troubled by the correctness variety of cases - separating keys by keywords will not work favorably when it hits University of reported 'placeCalifornia vs.' Currently script makes a cross product University of each reported place and an existing place, outputting Southern California case - find a column of boolean value way to indicate whether the reported place's coordinates fell within a place's geometric boundaries. One other way match University of going about this which we discussed is Southern California first (more specific ones first) - but how to first check if the reported place does fall within that place's boundaries. If it isn't, we'll go about the cross product method.generalize
* To add documentation 2017-03-27: ** http://mcnairWriting code for university matches - decided to go through keys instead of each dataitem.bakerinstituteUse keywords in each key to go through the dataitem - misspellings are currently unaccounted for.org/wiki/PostGIS_Installation** http://mcnair.bakerinstitute.org/wiki/Urban_Start-up_Agglomeration
*Relevant File paths2017-03-22:*Read string matching & calculating distance, below are relevant links*E[http:\McNair\Projects\Agglomeration\TestGIS//www.cs.sqlcmu.edu/~wcohen/postscript/ijcai-ws-2003.pdf]**Z[http:\VentureCapitalData\SDCVCData\vcdb2\ProecssingCoLevelSimple//web.archive.sql**Zorg/web/20081224234350/http:\VentureCapitalData\SDCVCData\vcdb2\CitiesWithGT10Active//www.dcs.shef.ac.uk/~sam/stringmetrics.txthtml]
====9/26/2017 TUESDAY ''9AM-12PM03-22:* Talked to Julia about universal matcher, want to combine all University of California''====s to University of California, The Regents of* Created a table that maps a state Converted crunchbase2013 data from mySQL to PostgreSQL, but having trouble with the database name.** http://mcnair.bakerinstitute.org/wiki/PostGIS_Installation#Translating_Table_names_to_corresponding_States* Added more GISlast table -information (functionscb_relationships, realm & outliers to consider)complains about syntax error at or near some places - but generally all tables exist in database called crunchbase** http://mcnair.bakerinstitute.org/wiki/Urban_StartFederal Grant Data XML Parser was run -up_Agglomeration#GIS_Resources* Visualization the three output textfiles can be found in PostGIS or connecting to ArcGIS for visualization (import/export data)* Spatial indexing:** httpE://revenant.ca/www/postgis/workshop/indexing.html\McNair\Projects\Federal Grant Data\NSF
...====10/2/2017 MONDAY ''4PM-6PM''====* Talked to Harrison & Peter regarding ArcGIS** Currently have points plotted on Houston** Trouble interpreting geometry type, as currently reads in from text file** Documents located in : E:\McNair\Projects\Agglomeration\HarrisonPeterWorkArcGIS* Attempted to install PostGIS spatial extention from PostgreSQL but getting 'spatial database creation failed' error message.** Referenced instructions03-16: *** https://www.gpsfiledepot.com/tutorials/installing-and-setting-up-postgresql-with-postgis/Further documented [[University Patent Matching]]*** http://www.bostongis.com/PrinterFriendly.aspx?content_name=postgis_tut01Finished writing XML Parser
====10/3/2017 TUESDAY ''10AM-12PM & 1PM03-215:30PM''====* Installed PostGIS & is now visible Todo: write a wikipage on possible input/output info on pgAdmin IIIstring matcher* Wrote part of XML parser, extracted yearly data into E:\McNair\Projects\Federal Grant Data\NSF\NSF Extracted Data (up to year 2010)
* ArcGIS (connect to postgis database)2017-03-14:** 1) Open ArcMap** 2) Either open blank or open existing file/project** 3) Click on 'Add Data' button with a cross and a yellow diamond (under Selection toolbar)** 4) Go Started pulling academy cases but there are too many cases to the top-most directory by pressing on the arrow that points left-then-up (on the left worry about, in terms of institution of home button)** 5) Click on 'Database Connections'** 6) Click on 'Add Database Connection' (if Connection to localhostinterest.sde) does not exist already)** 7) Fill A document is located in the following fieldsE:\McNair\Projects\University Patents\academies_verify_cases.txt*** Database Platform: PostgreSQL*** Instance: localhost*** User name: postgres*** Password: *** Database: tigertest** 8) Press 'OK'** 9) Now you'll have 'Connection Need Julia/Meghana to localhostlook through the hits and see which are relevant & extract pattern from there.sde' in your Database Connections** 10) Double click on 'Connection to localhostHaving trouble outputting txt file without double quotes around every line.sde'** 11) Double click on the table Thinking that one text file should be output for all keywords instead of interest** 12having one each, to avoid overlap (ex) Click 'Finish'** 13) You'll see information populated on mapCOLLEGE and UNIVERSITY are both keywords; ALBERT EINSTEIN COLLEGE OF YESHIVA UNIVERSITY will be hit twice if it were counted as two separate instances, as one accounting for COLLEGE and the other for UNIVERSITY) - either in the form of the 'Layers'*** Tested with: tigertest.publicif-elseif statements or one big regex check.copointplacescontains
* On running & altering Oliver's script2017-03-13: ** LocationFor University Patent Data Matching - matched SCHOOL (output: E:\McNair\Projects\OliverLovesCircles\src\pythonUniversity Patents\vc_circles.py** Ed manipulated file names so that underscores would replace dots (St.Louis --> St_Louisschool_pulled_from_assignee_list_USA)** Takes in instances and sweep times as part of the argument, but not impactful as those variables are hardcoded in the script** Ran vc_circles.py with the following variables with changed values:*** SWEEP_CYCLE_SECONDS = 10 matched INSTITUTE(used to be 30)*** NUMBER_INSTANCES = 16 (used to be 8)** New output to be found in: E:\McNair\Projects\OliverLovesCirclesUniversity Patents\outinstitute_pulled_from_assignee_list_USA). * [[University Patent Matching]] * To be worked on later: Grant XML parsing & general name matcher
====10/9/2017 MONDAY''3PM-6PM''====03-08:* TODO'SWrote regex pattern that identifies all "university" matchings - can be found in E:\McNair\Projects\University Patents\university_pulled_from_assignee_list_USA -- is an output file** Downloading data onto tigertestTalked to Sonia, but didn't come to solid conclusion on identifying whether key words associate with city or country by running a python function*** RoadOutput sql tables from finished run of Jeemin_FDATrial_as_key_data_ripping.py *** Railway*** Coastline*** Instructions: http://mcnairRan through assigneelist_USA.txt to see how many different ways UNIVERSITY could be spelled wrong.bakerinstituteThere were many.org/wiki/PostGIS_Installation#Bulk_Download_TIGER_Shapefiles** Configure census data from American Community Survey (ACS)*** 1) Work out what data is Tried to logic through creating a pattern that could catch all different versions of our interest (confirm ACS)*** 2) Determine appropriate shape file unit: **** census block vsUNIVERSITY. census block group vs. census track*** 3) Load into tigertestDiscuss further on whether UNIVERSITIES and those that include UNIVERSITIES but include INC in the end should be pulled as relevant information
* Done2017-03-06:*[[Installing python in a database]]* Downloaded data from https://www.censusAdded building Python function section to [[Working with PostgreSQL]] at the bottom of the page.gov/cgi-bin/geo/shapefiles/index.php tl_2017_us_coastline -- 4209 tl_2017_us_primaryroads -- 11574 tl_2017_us_rails -- 176237** Link found to potentially download ACS data: https://www.census.gov/geo/maps-data/data/tiger-Ran FDA Trial dataripping again, as the text output files were wiped.html*** But most files Plan on it come discussing with Julia and Meghana again about pulling universities and other relevant institutions from the Assignee List USA.gdb extension * Talked to Sonia about pulling city, state, zipcode information, hence python was installed in a database. Will work with Sonia on Wednesday afternoon and not .shpsee how best a regex function could be implemented
====10/10/2017 TUESDAY''9AM-12PM''====*Discoveries/ Struggles regarding.gdb to .shp file conversion:** Esri Production Mapping (costly)*** License needs to be purchasesd: http://www.esri.com/software/arcgis/extensions/production03-mapping/pricing** Use ogr2ogr from gdal package*** https03://gis.stackexchange.com/questions/14432/migrating-geodatabase-data-into-postgis-without-esri-apps*** Command: ogr2ogr -f "ESRI Shapefile" [Destination of shapefile] [path Attempted to gdb file]*** Problem installing gdaloutput sql tables
====10/16/2017 MONDAY''4PM-6PM''====* Exported maps of points from the Bay Area each year. ** Map used location: E03-01:\McNair\Projects\Agglomeration\HarrisonPeterWorkArcGIS\Jeemin_Bay_Area Points_Every_Year\BayAreaEveryYearMap** Zoom scale: 1:650Started re-running Jeemin_FDATrial_as_key_data_ripping.000* Location of Bay Area Points png files: E:\McNair\Projects\Agglomeration\HarrisonPeterWorkArcGIS\Jeemin_Bay_Area Points_Every_Yearpy
====10/23/2017 MONDAY''4PM-6PM''====02-24:* Talked to Ed with Peter & Oliver about upcoming tasks & projectsContinued working on producing multiple tables - first two are done.* Loaded acs_place table 2017 (does not contain population) Was working on tigertestlocation, as there are multiple location tags per location.** SQL commands used:
DROP TABLE acs_place2017-02-22:* Finished Jeemin_FDATrial_as_key_data_ripping.py (E:\McNair\Projects\FDA Trials\Jeemin_Project\Jeemin_FDATrial_as_key_data_ripping.py), which outputs to E:\McNair\Projects\FDA Trials\Jeemin_Project\general_data_ripping_output.txt;TODO: output four different tables & replace the write in the same for-loop as going through each file
CREATE TABLE acs_place (2017-02-20: USPS varchar(5)* Continued working on Jeemin_FDATrial_as_key_data_ripping.py to find tags and place all of those information in a list. The other zipcode file did not finish executing after 2+ hours of running it - considering the possibility of splitting the record file into smaller bits, GEOID varchar(30), ANSICODE varchar(30), NAME varchar(100), LSAD varchar(30), FUNCSTAT varchar(10), ALAND varchar(30), AWATER varchar(30), ALAND_SQMI varchar(30), AWATER_SQMI varchar(30), INTPTLAT varchar(30), INTPTLONG varchar(30) );or running the processing on a faster machine.
2017-02-17:* Completed code for counting the number of occurrences for each unique zipcode. (currently titled & located: E:\McNair\Projects\FDA Trials\Jeemin_Project\Jeemin_Running_File.py). It has been running for 20+min because of the comprehensive XML data files. Meanwhile started coding to create a dictionary with the keys corresponding to each unique trial ID, mapped to every other information (location, sponsors, phase, drugs ...etc.) (currently titled & located: E:\McNair\Projects\FDA Trials\COPY acs_place FROM '/bulk/2017_Gaz_place_nationalJeemin_Project\Jeemin_FDATrial_as_key_data_ripping.py).txt'; --COPY 29578
* TODO2017-02-15:** Find acs place 2016 Discussed with Catherine what to do with FDA Trial data for population** Find larger acs and decided to have a dictionary with zip-codes as keys and number of trials occurred in that zipcode as values. Was still attempting to loop through the files without the code having to exist in the same directory as the XML files. Plan to write to excel via tsv, ideally at with zip-code as one column and # of occurrence as the place level** Provide more documentation on POSTGIS & geocodingother.
...2017-02-13:* Goals (for trials): 1) Build ER Diagram 2) For each entity, get XML snippet 3) Build a parser/ripper for single file; the python parser can be found at: E:\McNair\Projects\FDA Trials\Jeemin_Project
====10/30/2017 MONDAY''4PM-6PM''====02-08:* Downloaded data Attempted to come up with possible cases for locating the description of accelerators - pick up from ACS, to be continuedextracting bodies of text from the about page (given that it exists)* File path: E:\McNair\Projects\Agglomeration\ACS_Downloaded_Data[[Trial Data Project]]
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[[Jeemin Sim]] [[Work Logs]] [[Jeemin Sim (WorkLog)|(log page)]] ===Spring 2018=2/6/==2017 MONDAY ''2PM-6PM''01-11:*Was briefed on [[Urban Start-up Agglomeration and Venture Capital Investment]]*Going forward - running regressions in R in PostgreSQL and with desired layers (instead of levels) ===Fall 2017=== <onlyinclude> 2017-12-05:* Uploaded tables with KML files in TIF folder in bulk(E:) drive** Allegheny County** Atlanta** Chicago** Columbus, OH** Set up wikiPage & remote desktopDublin, OH** Vermont** Washington, D.C. * Started working on python version of web crawlerUpdated documentation for: ** http://www.edegan. So far it successfully prints out a catchphrasecom/wiki/ description TIF_Project#Uploading_TIF_Data_onto_database_.28tigertest.29 * shp2pgsql needs to be installed to upload Shapefiles to PostgreSQL database** applies for one websiteHouston, TX and Dallas, TX** DONE 2017-12-04:* To upload KML file into database with specified table name: researcher@McNairDBServ:/bulk/tigertest$ ogr2ogr -f PostgreSQL PG:"dbname=tigertest" chicagotif.kml -nln chicagotif* chicagotif table now resides in tigertest database 2017-11-30:* Displayed map with TIF districts and startups* Location: E:\McNair\Projects\Agglomeration\TIF\McNair_Color_Chicago_TIF_and_startups. To be worked onpng* Added information and steps to ArcMap/ArcGIS documentation page* Create a project page for 'Working with POSTGIS' and add instructions for uploading KML file onto POSTGIS** Command used : *** Logged in as : researcher@McNairDBServ /bulk/tigertest$ ogr2ogr -f PostgreSQL PG:"dbname=tigertest" chicagotif. The python kml * chicago TIF kml file currently downloaded in tigertest with a table name of Layer0** Figure out how to change layer name while loading kml file can be found ** Instructions pulled from : http://wiki.wildsong.biz/index.php/Loading_data_into_PostGIS#Loading_data_from_KMZ_files 2017-11-28:* Created and edited [[ArcMap / ArcGIS Documentation]]* Plotted points for TIFS and Startups in Chicago inone map.** Location: E:\McNair\Projects\AcceleratorsAgglomeration\Python WebCrawlerTIF\webcrawlerpythonJeemin_Chicago_TIF_and_Startups_Attempt1* Used https://mygeodata.cloud/result to convert from KML file to CSV (which was then saved as txt file to be uploaded onto ArcMap)* Text files located in Local Disk (C:) Drive 2017-11-27:*Download Chicago TIF data 2017-11-13:* 2017-11-09: * Notes on data downloaded:** Year 2010-2012 data are based on total population, not 25 yrs or over (case for all other tables)*** Record appears five times total, with same exact column name***For exmaple: 'Total; Estimate; High school graduate (includes equivalency)' appears five times, with different values.* TODO:** Make Projects page for ACS Data***[[American Community Survey (ACS) Data]] 2017-11-07:*Yesterday, narrowed down columns of interest from ACS_S1501_educationattain_2016 table.py
* psql table formula:Discussed the need to maintain venture capital database.
* Useful functions for spatial joins:
* Continue reading from: http://workshops.boundlessgeo.com/postgis-intro/geography.html
2017-04-12:*Relevant PostgreSQL CommandsFinishing up cleaning the columns for Federal Grant Data - NIH. The output excel files can be accessed at: '''E:\McNair\Projects\dt *Federal Grant Data\NIH\Grants Titled: Jeemin_combined_files 1986-2001.csv Jeemin_combined_files 2002-2012.*''' Show all tablescsv '''\q''' Exit table Jeemin_combined_files 2013-2015.csv
*Specifities/ Outliers to considerpsql table formula: New York (decompose) Princeton area (keep Princeton unique) Reston, Virginia (keep) San Diego (include La Jolla) Silicon Valley (all distinct)
2017-03-24:* Discussed with Julia & Meghana about university keys to use to count # of occurrences, including aliases and misspellings* Thoughts: to use a scoring metric with a key of UNIVERSITY OF CALIFORNIA SYSTEM, it should have a 'better' score when compared to MATHEMATICAL SCIENCES PUBLISHERS C/O UNIVERSITY OF CALIFORNIA BERKELEY or CALIFORNIA AT LOS ANGELES, UNVIERSITY OF than when compared to UNIVERSITY OF SOUTHERN CALIFORNIA, which may pose a challenge when attempting to implement this in a more general sense. In normalizing a string, strip "THE", "," and split words by spaces and compare each keyword from the need two strings. Deciding on which strings to maintain venture capital databasecompare will be another issue - length (within some range maybe) could be an option.* Federal Grant Data XML Parser was rerun - same output textfiles
2017-02-27:* Finished producing tables from Jeemin_FDATrial_as_key_data_ripping.py* Talked to Julia about LinkedIn data extracting - to be discussed further with Julia & Peter.* Started web crawler for Wikipedia - currently pulls Endowment, Academic staff, students, undergraduates, and postgraduates info found on Rice Wikipedia page.Can be found in : E:\McNair\Projects\University Patents\Jeemin_University_wikipedia_crawler.py
2017-02-06:
* Set up wikiPage & remote desktop.
* Started working on python version of web crawler. So far it successfully prints out a catchphrase/ description for one website. To be worked on. The python file can be found in: E:\McNair\Projects\Accelerators\Python WebCrawler\webcrawlerpython.py
[[Category:Work Log]]
