1 00:00:00,000 --> 00:00:04,166 HELLO AND THANK YOU FOR JOINING US FOR EDIRECT FOR PUBMED. 2 00:00:04,166 --> 00:00:08,532 THIS IS PART OF THE INSIDER'S GUIDE TO ACCESSING NLM DATA. 3 00:00:08,533 --> 00:00:14,366 MY NAME IS PETER SEIBERT AND I'M HERE WITH SARAH HELSON WHO WILL BE PRESENTING THIS THURSDAY'S SESSION 4 00:00:14,366 --> 00:00:20,466 AS WELL AS MIKE DAVIDSON, WHO IS THE MASTERMIND BEHIND THE INSIDER'S GUIDE 5 00:00:20,466 --> 00:00:26,599 TO ACCESSING NLM DATA. HE'LL BE PRESENTING PARTS 4 AND 5 NEXT WEEK AND IN TWO WEEKS. 6 00:00:26,600 --> 00:00:32,666 OVER THE COURSE OF THESE FIVE SESSIONS, WE'LL INTRODUCE YOU TO USING EDIRECT TO SEARCH FOR 7 00:00:32,666 --> 00:00:38,766 RETRIEVE AND MANIPULATE PUBMED DATA IN A UNIX ENVIRONMENT. 8 00:00:38,766 --> 00:00:42,332 THERE'S A LOT TO COVER, BUT WE'LL GO OVER THE BASICS AND GIVE YOU ENOUGH TO GET YOU STARTED 9 00:00:42,333 --> 00:00:45,899 WITH THE RESOURCES TO CONTINUE EXPLORING AND LEARNING ON YOUR OWN 10 00:00:45,900 --> 00:00:52,733 AND HOPEFULLY JOIN OUR NASCENT USER COMMUNITY, THAT YOU'LL SEE MORE TOWARD THE END OF THIS CLASS 11 00:00:52,733 --> 00:01:06,099 AND WE'LL TALK ABOUT THROUGHOUT THE ENTIRE COURSE. 12 00:01:06,100 --> 00:01:09,400 AS I SAID, THIS COURSE IS MADE UP OF FIVE SESSIONS. 13 00:01:09,400 --> 00:01:13,566 TODAY WE'RE GOING TO TALK ABOUT HOW WE USE EDIRECT TO GET DATA FROM PUBMED 14 00:01:13,566 --> 00:01:17,732 INCLUDING HOW TO DOWNLOAD FULL XML PUBMED RECORDS. 15 00:01:17,733 --> 00:01:22,199 NEXT TIME, SARAH WILL START TALKING ABOUT HOW TO EXTRACT SPECIFIC DATA ELEMENTS 16 00:01:22,200 --> 00:01:26,700 FROM XML RECORDS, AND ARRANGE THEM INTO A CUSTOM OUTPUT FORMAT. 17 00:01:26,700 --> 00:01:32,133 NEXT WEEK AT THIS SAME TIME, WE'LL GET INTO SOME MORE SPECIFIC WAYS TO FORMAT AND CUSTOMIZE 18 00:01:32,133 --> 00:01:37,599 OUR RESULTS, AND LOOK AT SOME UNIX TOOLS YOU CAN USE WHEN BUILDING YOUR SOLUTIONS. 19 00:01:37,600 --> 00:01:42,900 IN PART 4, MIKE WILL EXPLORE THE XTRACT CONDITIONAL ARGUMENTS THAT LET YOU FILTER YOUR OUTPUT. 20 00:01:42,900 --> 00:01:46,733 AND FINALLY, IN TWO WEEKS, WE PUT ALL THE PIECES TOGETHER 21 00:01:46,733 --> 00:01:52,833 AND LOOK AT SOME STRATEGIES FOR DEVELOPING AND BUILDING SOLUTIONS TO REAL-WORLD PROBLEMS. 22 00:01:52,833 --> 00:01:57,666 AND FOR THAT, WE'LL BUILD OFF THE USE CASES YOU PROVIDE IN THE NEXT COUPLE WEEKS. 23 00:01:57,666 --> 00:02:02,499 WE KNOW MOST OF YOU ALREADY HAVE EXPERIENCE SEARCHING IN PUBMED 24 00:02:02,500 --> 00:02:06,833 SO IT'S IMPORTANT TO UNDERSTAND THAT MANY OF THE TASKS AND CONCEPTS WE'LL BE TALKING ABOUT 25 00:02:06,833 --> 00:02:11,199 IN TODAYS SESSION AREN'T NECESSARILY COMPLETELY NEW TO YOU. 26 00:02:11,200 --> 00:02:12,933 FOR EXAMPLE: 27 00:02:12,933 --> 00:02:15,466 YOU ALREADY KNOW HOW TO SEARCH PUBMED 28 00:02:15,466 --> 00:02:19,766 AND RETRIEVE AND REVIEW RECORDS, BUT TODAY WE'RE GOING TO TEACH YOU NEW TECHNIQUES AND SYSTEMS 29 00:02:19,766 --> 00:02:24,066 TO ACCOMPLISH THAT TASK MORE EFFICIENTLY. 30 00:02:24,066 --> 00:02:28,966 THIS IS GOING TO LAY THE FOUNDATION FOR THE REST OF THE COURSE, WHERE WE'LL BUILD ON THESE NEW TECHNIQUES 31 00:02:28,966 --> 00:02:30,999 AND SHOW YOU HOW TO EXTRACT THE SPECIFIC DATA 32 00:02:31,000 --> 00:02:36,900 THAT YOU'RE LOOKING FOR IN CUSTOM OUTPUT FORMATS, WHICH IS SOMETHING YOU CAN'T DO 33 00:02:36,900 --> 00:02:39,500 IN THE PUBMED 34 00:02:39,500 --> 00:02:47,800 WEB INTERFACE. 35 00:02:47,800 --> 00:02:52,533 WE EXPECT MOST OF YOU HAVE TAKEN OUR "WELCOME TO E-UTILITIES FOR PUBMED" CLASS 36 00:02:52,533 --> 00:02:55,466 OR ARE AT LEAST FAMILIAR WITH THE CONTENT DISCUSSED IN THAT CLASS, 37 00:02:55,466 --> 00:03:00,299 BUT I'LL START WITH A BRIEF RECAP SO THAT EVERYONE IS ON THE SAME PAGE. 38 00:03:00,300 --> 00:03:03,700 WE'RE GOING TO BRIEFLY TALK ABOUT UNIX, WHICH IS THE ENVIRONMENT 39 00:03:03,700 --> 00:03:07,133 THAT WE'LL BE WORKING IN FOR THE NEXT TWO WEEKS. 40 00:03:07,133 --> 00:03:12,999 I'LL SHOW YOU TO CONTSTRUCT A PUBMED SEARCH USING THE ESEARCH COMMAND. 41 00:03:13,000 --> 00:03:18,666 WE'LL TALK ABOUT DOWNLOADING CITATION DATA FROM PUBMED RECORDS WITH EFETCH. 42 00:03:18,666 --> 00:03:24,866 AND I'LL FINISH UP BY TALKING ABOUT SCRIPTS, AND HOW TO COMBINE A SERIES OF COMMANDS INTO A DATA PIPELINE, 43 00:03:24,866 --> 00:03:31,066 TO GET THE MOST EFFICIENCY OUT OF EDIRECT. 44 00:03:31,066 --> 00:03:36,599 BEFORE I RECAP THE CONTENTS OF "WELCOME TO E-UTILITIES FOR PUBMED" I WANT TO REMIND YOU OF A GENERAL 45 00:03:36,600 --> 00:03:42,133 THEME IN THAT CLASS, THAT WILL BE OVERARCHING THESE NEXT FEW WEEKS OF CLASSES. 46 00:03:42,133 --> 00:03:46,833 E-UTILITIES IN GENERAL, AND EDIRECT MORE SPECIFICALLY, 47 00:03:46,833 --> 00:03:49,866 ARE BEST UTILIZIED TO GET THE DATA YOU NEED, 48 00:03:49,866 --> 00:03:58,866 IN EXACTLY THE FORMAT YOU NEED IT. PRECISION IN SEARCHING AND RETRIEVAL OF OUR DATABASES IS THE GOAL. 49 00:03:58,866 --> 00:04:03,232 WE'LL COME BACK TO THAT A LITTLE LATER ON, 50 00:04:03,233 --> 00:04:11,766 BUT FIRST, TO REVIEW THE "WELCOME TO E-UTILITIES" CLASS, I'LL PROVIDE A FEW DEFINITIONS, STARTING WITH 51 00:04:11,766 --> 00:04:17,832 WHAT IS AN API? API STANDS FOR APPLICATION PROGRAMMING 52 00:04:17,833 --> 00:04:23,933 INTERFACE, AND IT IS SET OF TOOLS TO BUILD SOFTWARE APPLICATIONS. 53 00:04:23,933 --> 00:04:27,766 BUILDING ON THAT GENERAL DEFINITION, THE NLM API 54 00:04:27,766 --> 00:04:35,999 SUITE E-UTILITIES IS A SET OF TOOLS, ROUTINES AND PROTOCOLS, THAT ALLOW YOU 55 00:04:36,000 --> 00:04:42,500 TO INTERACT DIRECTLY WITH THE DATA IN OVER TWO DOZEN NCBI DATABASES, INCLUDING PUBMED, 56 00:04:42,500 --> 00:04:49,166 PUBMED CENTRAL (PMC), AND THE MESH DATABASE. 57 00:04:49,166 --> 00:04:54,499 THE E-UTILITIES API IS JUST A SERIES OF RULES FOR QUERYING THE BACKEND 58 00:04:54,500 --> 00:04:59,833 OF NLM DATABASES, AND THOSE QUERIES ARE IN THE FORM OF A STANDARD URL. 59 00:04:59,833 --> 00:05:04,466 THE RESPONSES YOU GET TO THE QUERY DEPEND ON HOW YOU BUILD YOUR URL. 60 00:05:04,466 --> 00:05:09,132 YOU CHOOSE ONE OF NINE UTILITIES TO SPECIFY WHAT TYPE OF QUERY YOU'RE ASKING. 61 00:05:09,133 --> 00:05:14,533 AND YOU SELECT PARAMETERS TO DEFINE THE DETAILS OF YOUR QUERY. 62 00:05:14,533 --> 00:05:17,799 IDEALLY, YOU DON'T WANT TO CREATE THESE URLS BY HAND. WITH THE TIME SPENT, 63 00:05:17,800 --> 00:05:21,100 YOU MIGHT BE BETTER OFF JUST USING THE WEB VERSION 64 00:05:21,100 --> 00:05:23,666 OF PUBMED. 65 00:05:23,666 --> 00:05:29,366 WHAT YOU REALLY WANT TO DO IS USE E-UTILITIES IN A PROGRAMMING ENVIRONMENT 66 00:05:29,366 --> 00:05:34,832 TO COMBINE MULTIPLE QUERIES IN SEQUENCE, USING THE RESULTS OF ONE QUERY TO CREATE THE NEXT. 67 00:05:34,833 --> 00:05:38,499 A PROGRAMMING ENVIRONMENT ALSO GIVES YOU MORE OPTIONS FOR 68 00:05:38,500 --> 00:05:44,633 MANIPULATING THE OUTPUT, RATHER THAN JUST TAKING XML OR TEXT. 69 00:05:44,633 --> 00:05:48,399 WHICH IS WHY NCBI DEVELOPED EDIRECT. 70 00:05:48,400 --> 00:05:50,966 IT IS A SET OF TOOLS 71 00:05:50,966 --> 00:05:57,399 WITH THE E-UTILITIES CREATION RULES BUILT IN. IT ALSO INCLUDES A POWERFUL TOOL FOR EXTRACTING AND PARSING 72 00:05:57,400 --> 00:06:03,866 SPECIFIC DATA ELEMENTS FROM XML, AND WAS WRITTEN TO WORK IN A UNIX ENVIRONMENT. 73 00:06:03,866 --> 00:06:06,499 NOW IS A SAID EARLIER THAT WE'RE GOING TO OPEN UP THE CHAT AND THE PANEL WINDOWS, 74 00:06:06,500 --> 00:06:09,866 SO THAT WE COULD INTERACT A LITTLE BIT. AND RIGHT NOW, TO START OFF, WE'LL DO SOMETHING REALLY SIMPLE 75 00:06:09,866 --> 00:06:13,266 TO START OFF, WE'LL DO SOMETHING REALLY SIMPLE: IN YOUR PARTICIPANTS WINDOW 76 00:06:13,266 --> 00:06:18,299 IF YOU'VE WORKED AT ALL WITH UNIX, IN A UNIX ENVIRONMENT, PROGRAMMING, 77 00:06:18,300 --> 00:06:23,333 ON A SERVER, ANYTHING, GO AHEAD AND GIVE ME A GREEN CHECK 78 00:06:23,333 --> 00:06:27,866 AGAIN, IN YOUR PARTICIPANTS WINDOW, DOWN AT THE BOTTOM, YOU'LL SEE A FEW EMOTICONS. 79 00:06:27,866 --> 00:06:44,966 IF YOU'VE WORKED WITH UNIX, ARE FAMILIAR WITH IT IN ANY WAY, GIVE ME A GREEN CHECK. 80 00:06:44,966 --> 00:06:48,699 TERRIFIC, THANK YOU THOSE OF YOU WHO RESPONDED. AGAIN, THERE'S TWO WAYS 81 00:06:48,700 --> 00:06:52,433 THAT WE'RE GOING TO INTERACT TODAY, IN OUR CLASS. WELL, THERE'S ACTUALLY THREE, 82 00:06:52,433 --> 00:06:56,166 IF YOU REALLY ARE FEELING BRAVE AND WANT TO UNMUTE AND JUST START CHATTING, BUT OTHERWISE, 83 00:06:56,166 --> 00:06:59,899 YOU CAN TYPE IN THE CHAT BOX, 84 00:06:59,900 --> 00:07:05,100 OR YOU CAN USE ONE OF THE EMOTICONS IN OUR PARTICIPANTS PANEL 85 00:07:05,100 --> 00:07:14,366 AGAIN, THANK YOU. I'M GOING TO CLEAR THAT. 86 00:07:14,366 --> 00:07:20,032 SO UNIX IS AN OPERATING SYSTEM THAT ALLOWS YOU TO INTERACT DIRECTLY WITH THE COMPUTER. 87 00:07:20,033 --> 00:07:26,033 UNIX OPERATES VIA COMMAND-LINE INTERFACE, WHICH IS BASICALLY A TEXT PROMPT. YOU TYPE 88 00:07:26,033 --> 00:07:29,033 INSTRUCTIONS TO THE COMPUTER, TELL THE COMPUTER TO EXECUTE THOSE 89 00:07:29,033 --> 00:07:32,033 INSTRUCTIONS, AND THEN YOU WAIT FOR THE RESULTS. 90 00:07:32,033 --> 00:07:38,966 YOU MAY ALSO SEE A COMMAND-LINE INTERFACE REFERRED TO AS A SHELL OR TERMINAL. WHILE THESE TERMS ARE NOT 91 00:07:38,966 --> 00:07:45,899 EXACTLY SYNONYMOUS, FOR ALL INTENTS AND PURPOSES FOR TODAY'S CLASS, WE WILL USE THEM INTERCHANGEABLY. 92 00:07:45,900 --> 00:07:49,400 DEPENDING ON WHAT TYPE OF COMPUTER YOU'RE USING, YOU MAY HAVE DIFFERENT 93 00:07:49,400 --> 00:07:52,900 DEPENDING ON WHAT TYPE OF OPTIONS FOR WHICH TERMINAL YOU WANT TO USE. I'M ON A 94 00:07:52,900 --> 00:07:59,900 WINDOWS PC, SO I'VE DOWNLOADED THE FREE UNIX TERMINAL EMULATOR CYGWIN. 95 00:07:59,900 --> 00:08:05,500 IF YOU'RE USING A MAC OR LINUX MACHINE, YOU'RE PROBABLY ALREADY IN YOUR NATIVE 96 00:08:05,500 --> 00:08:12,800 OPERATING SYSTEM. REGARDLESS OF WHAT YOU'RE USING, IT ALL BOILS DOWN TO THE SAME THING: 97 00:08:12,800 --> 00:08:20,433 IT'S A PROMPT WHERE YOU CAN TYPE INSTRUCTIONS TO THE COMPUTER, EXECUTE THEM, AND SEE YOUR RESULTS. 98 00:08:20,433 --> 00:08:20,466 99 00:08:20,466 --> 00:08:30,132 SINCE WE'RE GOING TO BE JUMPING 100 00:08:30,133 --> 00:08:38,833 BETWEEN A FEW WINDOWS THIS IS MY 101 00:08:38,833 --> 00:08:45,666 PROMPT RUNNING THE E DIRECT. 102 00:08:45,666 --> 00:08:49,099 LIKE MOST OPERATING SYSTEMS IT'S 103 00:08:49,100 --> 00:08:50,566 BUILD TO WORK WIN FILES YOU CAN 104 00:08:50,566 --> 00:08:53,232 CREATE, REMOVE, DELETE, OPEN OR 105 00:08:53,233 --> 00:08:54,066 EDIT THEM. 106 00:08:54,066 --> 00:08:56,432 MANY OF THE FUNCTIONS OF UNIX 107 00:08:56,433 --> 00:08:58,233 WON'T BE NEEDED TODAY BUT CAN 108 00:08:58,233 --> 00:08:59,499 HELP YOU UNDERSTAND WHY THINGS 109 00:08:59,500 --> 00:09:01,466 DID OR DID NOT WORK. 110 00:09:01,466 --> 00:09:03,332 WE'LL BE USING THE FILE 111 00:09:03,333 --> 00:09:04,733 MANIPULATIONS TOOLS IN THE LATER 112 00:09:04,733 --> 00:09:06,399 SESSIONS AND I'LL SHOW YOU A 113 00:09:06,400 --> 00:09:13,100 LINK TO A QUICK UNIX WEBINAR IF 114 00:09:13,100 --> 00:09:14,900 YOU WANT TO GET MORE FAMILIAR. 115 00:09:14,900 --> 00:09:17,700 THE MODULAR DESIGN MEANS EACH 116 00:09:17,700 --> 00:09:19,633 SYSTEM IS SUPPOSED TO DO ONE 117 00:09:19,633 --> 00:09:20,966 THING VERY WELL AND PROGRAMMERS 118 00:09:20,966 --> 00:09:22,432 HAVE THEIR OWN PERSONAL TASTE 119 00:09:22,433 --> 00:09:23,699 AND DEVELOPED DIFFERENT TOOLS TO 120 00:09:23,700 --> 00:09:25,133 DO ALMOST THE SAME THING. 121 00:09:25,133 --> 00:09:27,266 THIS MEANS THERE ARE OFTEN 122 00:09:27,266 --> 00:09:29,666 MULTIPLE WAYS TO DO THE SAME 123 00:09:29,666 --> 00:09:55,499 TASK. 124 00:09:55,500 --> 00:09:58,100 IT CAN COMBINE MULTIPLE PROGRAMS 125 00:09:58,100 --> 00:09:58,433 TOGETHER. 126 00:09:58,433 --> 00:10:00,566 TO ENSURE WE'RE ALL OPERATING ON 127 00:10:00,566 --> 00:10:02,566 THE SAME SHEET OF MUSIC FOR THIS 128 00:10:02,566 --> 00:10:03,566 CLASS AND THE REST OF THE 129 00:10:03,566 --> 00:10:08,799 CLASSES IN THIS COURSE I'M GOING 130 00:10:08,800 --> 00:10:11,200 TO DEFINE A FEW TERMS WE'LL BE 131 00:10:11,200 --> 00:10:14,166 USING THROUGHOUT IN THE UNIX 132 00:10:14,166 --> 00:10:17,966 ENVIRONMENT. 133 00:10:17,966 --> 00:10:19,099 DEMANDS ARE INSTRUCTIONS BY A 134 00:10:19,100 --> 00:10:20,766 USE. 135 00:10:20,766 --> 00:10:23,632 SEEMS STRAIGHTFORWARD. 136 00:10:23,633 --> 00:10:25,166 THERE'S THE RUN COMMAND OR SAFE 137 00:10:25,166 --> 00:10:34,732 COMMAND. 138 00:10:34,733 --> 00:10:35,799 ARGUMENTS CAN GIVE THE COMMAND 139 00:10:35,800 --> 00:10:39,100 AND E-SEARCH IS THE COMMAND. 140 00:10:39,100 --> 00:10:44,566 THIS PUB MED IS THE ARGUMENT AND 141 00:10:44,566 --> 00:10:46,899 TELLS THE COMMAND WE'LL BE USING 142 00:10:46,900 --> 00:10:50,233 PUB MED AS THE DATABASE AND 143 00:10:50,233 --> 00:10:51,599 USING IT THROUGHOUT THE COURSE. 144 00:10:51,600 --> 00:10:57,633 IN OUR SECOND EXAMPLE E-INFO IS 145 00:10:57,633 --> 00:11:04,266 YOUR COMMAND AND WITH THIS DBS 146 00:11:04,266 --> 00:11:06,932 ARGUMENT WE'RE MODIFYING THE 147 00:11:06,933 --> 00:11:08,966 BEHAVIOR OF INFO TELLING IT WE 148 00:11:08,966 --> 00:11:14,999 WANT TO USE THE DBS OPTION WHEN 149 00:11:15,000 --> 00:11:16,300 WE USE THE COMMAND. 150 00:11:16,300 --> 00:11:17,066 DIFFERENT COMMANDS HAVE 151 00:11:17,066 --> 00:11:17,832 DIFFERENT ARGUMENT. 152 00:11:17,833 --> 00:11:23,199 SOME HAVE REQUIRED ARGUMENTS AND 153 00:11:23,200 --> 00:11:25,566 SOME OPTIONAL ARGUMENTS AND SOME 154 00:11:25,566 --> 00:11:28,066 DON'T TAKE ANY ARGUMENTS. 155 00:11:28,066 --> 00:11:29,532 I HAVE SPOKEN ABOUT THIS BEFORE 156 00:11:29,533 --> 00:11:31,666 BUT WE OFTEN WANT TO TAKE THE 157 00:11:31,666 --> 00:11:33,999 OUTPUT FROM ONE COMMAND AND USE 158 00:11:34,000 --> 00:11:35,500 IT FOR THE INPUT FOR ANOTHER 159 00:11:35,500 --> 00:11:37,500 COMMAND RATHER THAN RUNNING A 160 00:11:37,500 --> 00:11:38,800 COMMAND THAT SAVES THE OUTPUT TO 161 00:11:38,800 --> 00:11:43,366 A FILE THEN RUNNING THE SECOND 162 00:11:43,366 --> 00:11:46,866 FILE AS AN ARGUMENT WE CAN PIPE 163 00:11:46,866 --> 00:11:49,966 THEM TOGETHER USING THE UNIX 164 00:11:49,966 --> 00:11:52,632 FUNCTION IT'S OVER THE ENTER KEY 165 00:11:52,633 --> 00:11:54,766 OVER MORE KEY BOARDS. 166 00:11:54,766 --> 00:11:57,999 HIT SHIFT AND BACKSLASH. 167 00:11:58,000 --> 00:12:00,466 IT PIPES OR CHANNELS THE OUTPUT 168 00:12:00,466 --> 00:12:03,632 OF ONE COMMAND TO THE NEXT. 169 00:12:03,633 --> 00:12:05,866 LOOK AT THE ACTION THROUGH THE 170 00:12:05,866 --> 00:12:07,466 REST OF TODAY'S CLASS AND YOU'LL 171 00:12:07,466 --> 00:12:08,966 BE USING IT THROUGH THE REST OF 172 00:12:08,966 --> 00:12:13,332 THE COURSE. 173 00:12:13,333 --> 00:12:15,466 WHEN WORKING IN ANY PROGRAMMING 174 00:12:15,466 --> 00:12:16,432 LANGUAGE, YOU SHOULD BE READY 175 00:12:16,433 --> 00:12:18,066 FOR THE NEED FOR REPETITION AND 176 00:12:18,066 --> 00:12:19,299 TROUBLE SHOOTING. 177 00:12:19,300 --> 00:12:23,233 SOMETHING YOU'LL TRY TO DO WON'T 178 00:12:23,233 --> 00:12:24,199 INEVITABLY WORK AND YOU'LL HAVE 179 00:12:24,200 --> 00:12:25,900 TO FIGURE OUT WHY IT FAILED. 180 00:12:25,900 --> 00:12:28,633 WITH UNIX THE DETAILS MATTER 181 00:12:28,633 --> 00:12:32,033 IT'S SPACE AND CASE SENSITIVE. 182 00:12:32,033 --> 00:12:33,433 IF YOU DON'T DO IT IN THE 183 00:12:33,433 --> 00:12:35,999 CORRECT SYNTAX THE SCRIPT WON'T 184 00:12:36,000 --> 00:12:38,166 WORK AND A LOT OF TIMES IT WON'T 185 00:12:38,166 --> 00:12:39,566 TELL YOU WHAT YOU DID WRONG. 186 00:12:39,566 --> 00:12:41,099 THIS IS A LIVE CLASS SO YOU WILL 187 00:12:41,100 --> 00:12:46,933 SEE ME TYPING AND LIKELY GET THE 188 00:12:46,933 --> 00:12:48,699 EXACT MISTAKES AND SEE HOW I 189 00:12:48,700 --> 00:12:53,333 HAVE TO HANDLE THEM. 190 00:12:53,333 --> 00:12:55,633 JUST A COUPLE TIPS, TEST EARLY, 191 00:12:55,633 --> 00:13:00,299 OF THE OFTEN AND WITH 192 00:13:00,300 --> 00:13:02,600 INCREMENTAL CHANGES. 193 00:13:02,600 --> 00:13:04,533 IT COULD BE HARD TO FIGURE OUT 194 00:13:04,533 --> 00:13:08,299 WHAT LINE IS THE ROOT CAUSE OF 195 00:13:08,300 --> 00:13:08,866 FAILING. 196 00:13:08,866 --> 00:13:12,166 USE SMALL SETS OF DUMMY DATA 197 00:13:12,166 --> 00:13:14,199 PMIDs YOUR FAMILIAR WITH. 198 00:13:14,200 --> 00:13:17,333 YOU CAN ADD IN A SEARCH STRATEGY 199 00:13:17,333 --> 00:13:22,999 ARTIFICIALLY LIMITED BY DATE TO 200 00:13:23,000 --> 00:13:26,533 SHRINK THE RETRIEVAL. 201 00:13:26,533 --> 00:13:28,133 THE INTERNET IS A GREAT PLACE TO 202 00:13:28,133 --> 00:13:28,666 START. 203 00:13:28,666 --> 00:13:32,132 THERE ARE GREAT ESTABLISHED UNIX 204 00:13:32,133 --> 00:13:33,633 USER COMMUNITIES OUT THERE WITH 205 00:13:33,633 --> 00:13:36,333 NOT ONLY HOW-TO DOCUMENTATION 206 00:13:36,333 --> 00:13:39,666 BUT THOSE WHO ACTIVELY SEARCH 207 00:13:39,666 --> 00:13:43,066 QUESTIONS. 208 00:13:43,066 --> 00:13:45,999 ONE WE GET A LOT OF RESPONSE 209 00:13:46,000 --> 00:13:51,000 BACK IS FOR STACK OVERFLOW. 210 00:13:51,000 --> 00:13:55,700 SOME OF YOU WILL BE USING AN 211 00:13:55,700 --> 00:13:57,500 UNIX EMULATOR. 212 00:13:57,500 --> 00:14:03,300 I USE SEGWIN. 213 00:14:03,300 --> 00:14:04,466 COPYING AND TASTING IS 214 00:14:04,466 --> 00:14:04,832 DIFFERENT. 215 00:14:04,833 --> 00:14:06,599 HERE'S THE HOT KEYS FOR THAT. 216 00:14:06,600 --> 00:14:09,833 IF IT'S TOO DISTRACTING YOU CAN 217 00:14:09,833 --> 00:14:12,599 GO IN THE OPTIONS OF SEGWIN AND 218 00:14:12,600 --> 00:14:21,166 SET THEM YOURSELF. 219 00:14:21,166 --> 00:14:28,799 A TIP CONTROL-ALT-C WILL STOP IT 220 00:14:28,800 --> 00:14:30,866 AND IT WILL CANCEL YOU OUT. 221 00:14:30,866 --> 00:14:32,699 THE UP AND DOWN ARROWS CYCLE 222 00:14:32,700 --> 00:14:33,466 THROUGH YOUR HISTORY. 223 00:14:33,466 --> 00:14:36,332 YOU'LL SEE ME USING THESE A LOT 224 00:14:36,333 --> 00:14:38,433 AS WE ENTER OUR SCRIPTS INTO 225 00:14:38,433 --> 00:14:41,433 E-DIRECT AND RE-USE THEM OVER 226 00:14:41,433 --> 00:14:43,066 AND OVER AND THE CLEAR COMMAND. 227 00:14:43,066 --> 00:14:44,432 THIS WILL CLEAR YOUR SCREEN AND 228 00:14:44,433 --> 00:14:47,099 GIVE YOU A FRESH PALATE TO START 229 00:14:47,100 --> 00:14:49,100 OFF OF AND YOU DON'T NEED TO 230 00:14:49,100 --> 00:14:49,400 WORRY. 231 00:14:49,400 --> 00:14:51,466 IT RETAINS YOUR HISTORY SO IT 232 00:14:51,466 --> 00:14:52,799 WILL STILL CYCLE THROUGH THE 233 00:14:52,800 --> 00:14:54,766 LONG ARGUMENTS YOU'VE WRITTEN 234 00:14:54,766 --> 00:15:03,466 FOR E-DIRECT. 235 00:15:03,466 --> 00:15:04,732 SO WE WENT THROUGH A LOT OF THE 236 00:15:04,733 --> 00:15:16,566 OVERVIEW AND ADMINISTRATIVE 237 00:15:16,566 --> 00:15:17,932 TASKS AND LET YOU CATCH UP AND 238 00:15:17,933 --> 00:15:21,299 SEE IF THERE'S QUESTIONS TO THIS 239 00:15:21,300 --> 00:15:25,033 POINT. 240 00:15:25,033 --> 00:15:40,099 NOT SEEING ANY WE WILL CONTINUE. 241 00:15:40,100 --> 00:15:41,766 DOES ANYONE REMEMBER WHAT 242 00:15:41,766 --> 00:15:43,032 E-SEARCH DOES. 243 00:15:43,033 --> 00:15:44,999 YOU CAN UNMUTE IF YOU'RE FEELING 244 00:15:45,000 --> 00:15:46,366 BRAVE OR TYPE IN THE CHAT. 245 00:15:46,366 --> 00:15:48,166 DOES ANYONE HAVE A LAYMAN'S TERM 246 00:15:48,166 --> 00:15:50,432 FOR E-SEARCH YOU'RE WILLING TO 247 00:15:50,433 --> 00:16:15,799 SHARE? 248 00:16:15,800 --> 00:16:21,166 KATE SAYS ESEARCH FOR TREES 249 00:16:21,166 --> 00:16:22,832 UIDs. 250 00:16:22,833 --> 00:16:26,099 I'LL TELL YOU I'LL BE ASKING FOR 251 00:16:26,100 --> 00:16:27,000 PARTICIPATION THROUGHOUT THE 252 00:16:27,000 --> 00:16:28,266 CLASS TO FEEL FREE TO TYPE IN 253 00:16:28,266 --> 00:16:33,766 THERE OR UNMUTE. 254 00:16:33,766 --> 00:16:38,066 THE INTERACTION MAKES THE CLASS 255 00:16:38,066 --> 00:16:39,966 MORE FULFILLING FOR EVERYONE. 256 00:16:39,966 --> 00:16:44,399 SO WITH MY -- THANK YOU, NANCY. 257 00:16:44,400 --> 00:16:45,833 I WAS WAITING FOR SOMEONE TO CUT 258 00:16:45,833 --> 00:16:53,799 TO THE QUICK ON THAT ONE. 259 00:16:53,800 --> 00:16:59,766 IT MEETS YOUR SEARCH. 260 00:16:59,766 --> 00:17:05,332 THE PUB MED THE PMIDs MATCH A 261 00:17:05,333 --> 00:17:23,166 SEARCH QUERY. 262 00:17:23,166 --> 00:17:25,132 I'LL BE MOVING BETWEEN WINDOWS 263 00:17:25,133 --> 00:17:27,933 AND NOW I'LL GO INTO MY OWN 264 00:17:27,933 --> 00:17:29,233 DIRECT PROMPT AND WELL START 265 00:17:29,233 --> 00:17:40,099 WITH THE EXAMPLE WE'RE GOING TO 266 00:17:40,100 --> 00:17:46,933 SEARCH SEASON DEFECTIVE 267 00:17:46,933 --> 00:17:47,999 DISORDER. 268 00:17:48,000 --> 00:17:58,033 WE'LL TYPE E-SEARCH AS OUR 269 00:17:58,033 --> 00:17:59,966 COMMAND AND OUR FIRST ARGUMENT 270 00:17:59,966 --> 00:18:04,132 WILL TELL US WHAT DATABASE WE 271 00:18:04,133 --> 00:18:05,666 WANT TO QUERY. 272 00:18:05,666 --> 00:18:08,299 WE'LL BE WORKING IN PUB MED 273 00:18:08,300 --> 00:18:14,466 TODAY. 274 00:18:14,466 --> 00:18:15,966 THE NEXT ARGUMENT IS TO BUILD 275 00:18:15,966 --> 00:18:17,499 OUR QUERY. 276 00:18:17,500 --> 00:18:20,533 WE THE CITATIONS IN PUB MED 277 00:18:20,533 --> 00:18:23,199 DEALING WITH SEASONAL AFFECTIVE 278 00:18:23,200 --> 00:18:30,033 DISORDER. 279 00:18:30,033 --> 00:18:36,899 THEN WE HIT ENTER. 280 00:18:36,900 --> 00:18:39,933 I'LL RETRIEVE A SNIPPET WITH 281 00:18:39,933 --> 00:18:41,933 ITEMS WE'LL DISCUSS LATER BUT 282 00:18:41,933 --> 00:18:43,833 THE ONE I WANT TO DRESS IS THE 283 00:18:43,833 --> 00:18:46,733 COUNT 1,658 IN BETWEEN THE OPEN 284 00:18:46,733 --> 00:18:49,133 AND CLOSE COUNT ELEMENT IN THE 285 00:18:49,133 --> 00:18:50,499 XML. 286 00:18:50,500 --> 00:19:03,833 IF WE JUMP INTO PUB MED AND I 287 00:19:03,833 --> 00:19:07,866 CONDUCT THE SAME SEARCH, SEASON 288 00:19:07,866 --> 00:19:09,399 AFFECTIVE DISORDER YOU'LL SEE I 289 00:19:09,400 --> 00:19:12,000 WILL RETRIEVE THE SAME NUMBER OF 290 00:19:12,000 --> 00:19:12,733 CITATIONS. 291 00:19:12,733 --> 00:19:15,699 THEY'RE TWO SYSTEMS QUERYING THE 292 00:19:15,700 --> 00:19:17,766 SAME BACK END DATABASE. 293 00:19:17,766 --> 00:19:20,466 THEY'RE HITTING EXACTLY THE SAME 294 00:19:20,466 --> 00:19:23,766 DATA TO RETRIEVE THESE 295 00:19:23,766 --> 00:19:24,099 CITATIONS. 296 00:19:24,100 --> 00:19:28,233 GOING BACK TO OUR E-DIRECT 297 00:19:28,233 --> 00:19:30,533 PROMPT, ANOTHER ITEM I WANT TO 298 00:19:30,533 --> 00:19:32,533 DRAW YOUR ATTENTION TO IS THE 299 00:19:32,533 --> 00:19:36,633 WEB ENVIRONMENT AND THE QUERY 300 00:19:36,633 --> 00:19:37,233 KEY. 301 00:19:37,233 --> 00:19:39,366 WE'LL GET INTO THOSE LATER IN 302 00:19:39,366 --> 00:19:45,399 THE COURSE THIS WILL ALLOW YOU 303 00:19:45,400 --> 00:19:47,366 TO STRING MULTIPLE COMMANDS 304 00:19:47,366 --> 00:19:49,332 TOGETHER AND USE THE RESULTS OF 305 00:19:49,333 --> 00:19:52,299 ONE TO CREATE OTHER DEMANDS AND 306 00:19:52,300 --> 00:19:53,066 PROCESSES. 307 00:19:53,066 --> 00:19:55,432 YOU'LL NOTE THERE AREN'T ANY 308 00:19:55,433 --> 00:19:58,933 PMIDs RETURNED FROM THE SEARCH. 309 00:19:58,933 --> 00:20:00,733 THERE'S A REASON FOR THIS. 310 00:20:00,733 --> 00:20:02,866 IF YOUR RESULT SET IS HUGE YOU 311 00:20:02,866 --> 00:20:05,232 CAN HAVE HUNDREDS OF THOUSAND OF 312 00:20:05,233 --> 00:20:07,733 PMIDs SCROLLING DOWN THE PAGE. 313 00:20:07,733 --> 00:20:09,766 THIS SHOWS YOU THE SIZE OF YOUR 314 00:20:09,766 --> 00:20:12,432 RESULT SET AND LETS YOU DECIDE 315 00:20:12,433 --> 00:20:14,333 WHAT YOU WANT TO DO WITH IT AND 316 00:20:14,333 --> 00:20:17,366 TIES BACK TO A RECURRING THEME. 317 00:20:17,366 --> 00:20:20,599 YOU'LL WANT TO STEP SLOWING ONE 318 00:20:20,600 --> 00:20:23,233 STEP AT A TIME AND ANALYZE YOUR 319 00:20:23,233 --> 00:20:23,566 RESULTS. 320 00:20:23,566 --> 00:20:25,632 REMEMBER, WE CAN DO ALL THE SAME 321 00:20:25,633 --> 00:20:26,933 SEARCHS WE DO IN THE WEB VERSION 322 00:20:26,933 --> 00:20:29,933 OF PUB MED AND E-SEARCH. 323 00:20:29,933 --> 00:20:34,033 SO I'M GOING TO GO BACK TO PUB 324 00:20:34,033 --> 00:20:36,999 MED AND CLEAR MY SEARCH. 325 00:20:37,000 --> 00:20:41,900 SO IN PUB MED WE CAN RUN A 326 00:20:41,900 --> 00:20:43,800 SEARCH AND TAG TERMS AND 327 00:20:43,800 --> 00:20:46,700 RESTRICT OUR SEARCH TO CERTAIN 328 00:20:46,700 --> 00:20:47,200 FIELDS. 329 00:20:47,200 --> 00:20:48,433 FOR EXAMPLE, I'M LOOKING FOR ALL 330 00:20:48,433 --> 00:20:52,666 THE CITATIONS ABOUT MALARIA AND 331 00:20:52,666 --> 00:20:54,766 PUB MED BUT I WANT TO LIMIT THEM 332 00:20:54,766 --> 00:20:57,232 TO A SPECIFIC JOURNAL. 333 00:20:57,233 --> 00:20:59,233 IN MY CASE I'D LIKE TO STICK TO 334 00:20:59,233 --> 00:21:00,299 JAMA. 335 00:21:00,300 --> 00:21:07,066 IN PUB MED I WOULD ENTER MY 336 00:21:07,066 --> 00:21:08,632 SEARCH TERM AND TIE THAT 337 00:21:08,633 --> 00:21:20,899 TOGETHER WITH THE OPERATOR AND 338 00:21:20,900 --> 00:21:35,833 TAGGING IT WITH THE JOURNAL TAG. 339 00:21:35,833 --> 00:21:37,599 YOU'LL SEE THE SEARCH I WAS 340 00:21:37,600 --> 00:21:39,433 SEARCHING FOR AND LIMITED TO THE 341 00:21:39,433 --> 00:22:02,599 JOURNAL. 342 00:22:02,600 --> 00:22:05,233 I'LL CLEAR MY SCREEN SEARCH FOR 343 00:22:05,233 --> 00:22:06,633 CLARITY AND SAID I WANT TO 344 00:22:06,633 --> 00:22:09,433 SEARCH PUB MED FOR THE ARTICLES 345 00:22:09,433 --> 00:22:11,433 DEALING WITH THE TOPIC OF 346 00:22:11,433 --> 00:22:12,233 MALARIA. 347 00:22:12,233 --> 00:22:28,766 I WILL AGAIN SPECIFY MY SEARCH 348 00:22:28,766 --> 00:22:32,499 TO PUB MED AND BUILD THE QUERY 349 00:22:32,500 --> 00:22:34,033 AGAIN AS MY NEXT ARGUMENT. 350 00:22:34,033 --> 00:22:37,133 I'M LOOKING FOR MALARIA WITH 351 00:22:37,133 --> 00:22:38,733 TOPICS OF MALARIA AND RESTRICT 352 00:22:38,733 --> 00:23:04,266 THEM TO THE JOURNAL JAMA. 353 00:23:04,266 --> 00:23:07,566 AND MANAGE THE RESULTS BY SIZE 354 00:23:07,566 --> 00:23:08,199 RESTRICTION. 355 00:23:08,200 --> 00:23:11,166 SAY I WANT TO MODIFY MY PREVIOUS 356 00:23:11,166 --> 00:23:12,999 SEARCH AND GET ARTICLES 357 00:23:13,000 --> 00:23:15,666 PUBLISHED BETWEEN 2015 AND 2017. 358 00:23:15,666 --> 00:23:18,399 IF YOU'RE FAMILIAR WITH SEARCHS 359 00:23:18,400 --> 00:23:20,466 IN PUB MED I CAN DO THIS BY 360 00:23:20,466 --> 00:23:21,799 WRITING THE DATE RESTRICTION 361 00:23:21,800 --> 00:23:24,700 INTO MY QUERY ARGUMENT USING THE 362 00:23:24,700 --> 00:23:31,233 PUBLICATION TAG BUT THERE'S A 363 00:23:31,233 --> 00:23:31,866 DATE RANGE. 364 00:23:31,866 --> 00:23:34,299 THIS CAN BE USEFUL IF YOU HAVE A 365 00:23:34,300 --> 00:23:37,000 CAREFULLY CONSTRUCTED SEARCH 366 00:23:37,000 --> 00:23:38,566 STRING BUT WANTED TO PUT 367 00:23:38,566 --> 00:23:40,032 ARTIFICIAL DATE RESTRICTIONS FOR 368 00:23:40,033 --> 00:23:40,499 TESTING. 369 00:23:40,500 --> 00:23:43,100 AS I MENTIONED BEFORE, RATHER 370 00:23:43,100 --> 00:23:44,400 THAN RETYPING MY PREVIOUS DEMAND 371 00:23:44,400 --> 00:23:46,533 I'M GOING TO USE THE UP AND DOWN 372 00:23:46,533 --> 00:23:47,766 ARROWS TO PULL THE LAST COMMAND 373 00:23:47,766 --> 00:23:49,499 I EXECUTED BACK TO MY PROMPT. 374 00:23:49,500 --> 00:23:51,600 I'LL DO THAT SEARCH AGAIN FOR 375 00:23:51,600 --> 00:23:53,866 MALARIA AND JAMA AND NOW CAN HE 376 00:23:53,866 --> 00:24:00,766 HAD IT AND RE-RUN IT AND USE THE 377 00:24:00,766 --> 00:24:02,799 ARROW KEYS TO EDIT EARLIER 378 00:24:02,800 --> 00:24:03,433 COMMANDS. 379 00:24:03,433 --> 00:24:40,499 I'LL BRING UP MY I'M USING THE 380 00:24:40,500 --> 00:25:03,200 PUBLICATION DATE AND MY MAXIMUM 381 00:25:03,200 --> 00:25:05,166 DATE AT THE CURRENT CAREER 2017 382 00:25:05,166 --> 00:25:17,132 AND WE'LL CONDUCT THE SEARCH. 383 00:25:17,133 --> 00:25:19,466 IF I GO UNDER MY PUBLICATION 384 00:25:19,466 --> 00:25:22,066 DATES USING THE FILTER ON THE 385 00:25:22,066 --> 00:25:26,566 LEFT-HAND SIDE WE'LL RESTRICT 386 00:25:26,566 --> 00:25:28,399 THAT FROM 2015 TO THE CURRENT 387 00:25:28,400 --> 00:25:30,500 YEAR INCLUSIVE. 388 00:25:30,500 --> 00:25:32,233 BY THAT FILTER WHICH YOU'LL SEE 389 00:25:32,233 --> 00:25:36,199 WE GET 10 RESULTS AND IF YOU 390 00:25:36,200 --> 00:25:37,700 COME UNDER SEARCH RESULTS YOU'LL 391 00:25:37,700 --> 00:25:39,066 SEE WHAT THE SEARCH STRING WOULD 392 00:25:39,066 --> 00:25:42,166 BE FOR THAT PDAT RANGE AND WE'LL 393 00:25:42,166 --> 00:26:07,832 SEE IF THE RESULTS ARE THE SAME. 394 00:26:07,833 --> 00:26:09,466 HI, BARBARA. 395 00:26:09,466 --> 00:26:10,999 YOU ASKED HOW DID YOU MAKE THE 396 00:26:11,000 --> 00:26:12,466 PREVIOUS USE COMMAND APPEAR AT 397 00:26:12,466 --> 00:26:13,566 THE NEW PROMPT. 398 00:26:13,566 --> 00:26:17,799 NOT CLEAR HOW THIS IS DONE. 399 00:26:17,800 --> 00:26:19,833 SO I'M USING MY UP AND DOWN 400 00:26:19,833 --> 00:26:22,466 ARROWS ON MY KEY BOARD TO CYCLE 401 00:26:22,466 --> 00:26:24,599 THROUGH MY PREVIOUS COMMANDS BUT 402 00:26:24,600 --> 00:26:25,833 THIS MEANS THAT I WILL HAVE 403 00:26:25,833 --> 00:26:29,366 TYPED THEM IN PRIOR SO EVERY 404 00:26:29,366 --> 00:26:31,766 TIME YOU START A NEW SESSION 405 00:26:31,766 --> 00:26:33,532 YOUR HISTORY WILL BE CLEAR UNTIL 406 00:26:33,533 --> 00:26:34,999 YOU START ENTERING COMMANDS IN 407 00:26:35,000 --> 00:26:36,800 HERE THEN YOU CAN CYCLE THROUGH 408 00:26:36,800 --> 00:26:37,300 THEM. 409 00:26:37,300 --> 00:26:44,533 HOPE THAT MAKES THAT CLEAR. 410 00:26:44,533 --> 00:26:46,666 SO THAT WORKS VERY WELL AND 411 00:26:46,666 --> 00:26:47,699 RETRIEVES WHAT WE'RE LOOKING FOR 412 00:26:47,700 --> 00:26:49,900 BUT IF YOU'RE LIKE ME THE LONG 413 00:26:49,900 --> 00:26:51,933 STRING OF TEXT CAN GET HARD TO 414 00:26:51,933 --> 00:26:56,766 READ. 415 00:26:56,766 --> 00:26:58,799 IT MAKES SENSE IF WE CAN BREAK 416 00:26:58,800 --> 00:27:01,033 IT UP INTO LOGICAL LINES IN 417 00:27:01,033 --> 00:27:05,366 BREAK POINTS FOR THE DIFFERENT 418 00:27:05,366 --> 00:27:06,299 TYPES OF THE COMMAND. 419 00:27:06,300 --> 00:27:09,566 THE BACKSLASH TELLS UNIX THE 420 00:27:09,566 --> 00:27:11,999 COMMAND DOESN'T DONE YET. 421 00:27:12,000 --> 00:27:14,033 WHEN I TYPE ENTER IT EXPECT THE 422 00:27:14,033 --> 00:27:15,699 REST OF THE COMMAND TO COME AND 423 00:27:15,700 --> 00:27:17,800 I TYPE IT AND HIT ENTER AND IT 424 00:27:17,800 --> 00:27:18,866 WILL EXECUTE. 425 00:27:18,866 --> 00:27:20,766 THIS CAN BE USEFUL WHEN YOU'RE 426 00:27:20,766 --> 00:27:22,299 TYPING AND ENTERING BLOCKS OF 427 00:27:22,300 --> 00:27:24,566 CODE AS YOU SEE MANY EXAMPLES IN 428 00:27:24,566 --> 00:27:29,499 THE HOMEWORK AND SOLUTIONS WE 429 00:27:29,500 --> 00:27:31,066 USE THAT QUITE A BIT TO MAKE IT 430 00:27:31,066 --> 00:27:39,166 MORE USER HUMAN READABLE. 431 00:27:39,166 --> 00:27:40,766 YOU CAN PUT THE WHOLE COMMAND ON 432 00:27:40,766 --> 00:27:42,466 THE SAME LINE JUST MAKE SURE YOU 433 00:27:42,466 --> 00:28:09,199 REMOVE THE ADDITIONAL BACKSLASH. 434 00:28:09,200 --> 00:28:10,633 YOU CAN SEE THE PROMPT COMES 435 00:28:10,633 --> 00:28:11,299 BACK UP. 436 00:28:11,300 --> 00:28:17,200 SORRY ABOUT THAT. 437 00:28:17,200 --> 00:28:18,633 THERE YOU SEE MY ORIGINAL SEARCH 438 00:28:18,633 --> 00:28:21,233 AND I'M SORRY I'LL JUST TYPE 439 00:28:21,233 --> 00:28:31,699 THIS IN MYSELF. 440 00:28:31,700 --> 00:28:35,600 AND I'M KEEPING THAT TO PDAT AND 441 00:28:35,600 --> 00:28:39,400 MY RANGES ARE STILL 2015 TO 2017 442 00:28:39,400 --> 00:28:59,566 INCLUSIVE. 443 00:28:59,566 --> 00:29:01,432 THERE YOU CAN SEE THE ERRORS YOU 444 00:29:01,433 --> 00:29:03,466 CAN MAKE IN A LIFT PROMPT WHICH 445 00:29:03,466 --> 00:29:19,366 IS USEFUL AS WELL. 446 00:29:19,366 --> 00:29:21,066 SO WE'RE ABOUT TO DO THE FIRST 447 00:29:21,066 --> 00:29:22,366 EXERCISE BUT BEFORE WE DO 448 00:29:22,366 --> 00:29:23,832 THERE'S THE FIRST ITEM WE NEED 449 00:29:23,833 --> 00:29:24,599 TO DISCUSS. 450 00:29:24,600 --> 00:29:27,033 THESE ARE WITHIN THE SEARCH 451 00:29:27,033 --> 00:29:27,933 STRENGTH. 452 00:29:27,933 --> 00:29:29,933 IF YOU'VE TAKEN OUR PUB MED 453 00:29:29,933 --> 00:29:32,499 CLASSES YOU KNOW WE GENERALLY 454 00:29:32,500 --> 00:29:34,333 SUGGEST AVOIDING QUOTATION MARKS 455 00:29:34,333 --> 00:29:37,699 SINCE THEY TURN OFF AUTOMATIC 456 00:29:37,700 --> 00:29:39,866 TERM MAPPING WHICH IS USEFUL 457 00:29:39,866 --> 00:29:42,699 WITHIN PUB MED AND GENERALLY IT 458 00:29:42,700 --> 00:29:44,600 FUNCTIONS DIFFERENTLY THAN WHAT 459 00:29:44,600 --> 00:29:46,433 YOU'RE USED TO IN A STANDARD 460 00:29:46,433 --> 00:29:47,999 SEARCH WEB ENGINE. 461 00:29:48,000 --> 00:29:49,133 HOWEVER, THERE ARE TIMES WHEN 462 00:29:49,133 --> 00:29:51,133 YOU NEED TO DO A SEARCH OF A 463 00:29:51,133 --> 00:29:53,066 PARTICULAR TERM IN PUB MED AND 464 00:29:53,066 --> 00:30:00,066 WANT TO ENCLOSE IT IN QUOTES. 465 00:30:00,066 --> 00:30:01,999 SAY WE WANT TO ASK A QUESTION 466 00:30:02,000 --> 00:30:03,500 ABOUT CANCER IN THE JOURNAL 467 00:30:03,500 --> 00:30:05,700 SCIENCE AND I'LL JUMP INTO PUB 468 00:30:05,700 --> 00:30:07,466 MED SO YOU CAN SEE WHAT HAPPENS 469 00:30:07,466 --> 00:30:26,766 WHEN WE DO THIS. 470 00:30:26,766 --> 00:30:31,466 YOU DECIDE IT'S SCIENCE AND I 471 00:30:31,466 --> 00:30:33,899 TAG THAT WITH JOURNAL BECAUSE I 472 00:30:33,900 --> 00:30:37,366 ONLY WANT ARTICLES FROM THAT 473 00:30:37,366 --> 00:30:38,532 JOURNAL. 474 00:30:38,533 --> 00:30:56,599 AND I SEARCH. 475 00:30:56,600 --> 00:30:58,433 WHILE I SEE THE JOURNAL SCIENCE 476 00:30:58,433 --> 00:31:00,133 LISTED I SEE OTHER JOURNALS 477 00:31:00,133 --> 00:31:04,199 BEING RETRIEVED AGAINST BECAUSE 478 00:31:04,200 --> 00:31:07,233 SCIENCE IS USED AS AN 479 00:31:07,233 --> 00:31:09,699 ALTERNATIVE TITLE. 480 00:31:09,700 --> 00:31:11,366 SO WE WANT TO LIMIT THIS JUST TO 481 00:31:11,366 --> 00:31:12,766 THE JOURNAL SCIENCE AND I DO 482 00:31:12,766 --> 00:31:16,166 THAT IN THE PUB MED WEB 483 00:31:16,166 --> 00:31:24,099 INTERFACE BY QUOTING. 484 00:31:24,100 --> 00:31:26,300 I COME UNDER MY DETAILS JUST TO 485 00:31:26,300 --> 00:31:29,666 CHECK MY WORK AND STILL GETTING 486 00:31:29,666 --> 00:31:31,766 TO CANCER AND NOW I'VE LIMITED 487 00:31:31,766 --> 00:31:43,099 JUST TO THE JOURNAL SCIENCE. 488 00:31:43,100 --> 00:31:48,833 THIS CAN BE TRICKY IN E DIRECT. 489 00:31:48,833 --> 00:31:52,866 BECAUSE OUR QUERY IS ALREADY EN 490 00:31:52,866 --> 00:31:55,599 CLOSED IN QUOTES AND UNIX IS 491 00:31:55,600 --> 00:31:57,000 GOING TO GET CONFUSED WHERE THE 492 00:31:57,000 --> 00:32:11,333 SEARCH STRING ENDS. 493 00:32:11,333 --> 00:32:14,333 IF YOU HAVE TO USE QUOTES USE A 494 00:32:14,333 --> 00:32:17,266 BACKSLASH IT TELLS UNIX TO TREAT 495 00:32:17,266 --> 00:32:18,732 THE QUOTATION MARKS AROUND 496 00:32:18,733 --> 00:32:22,666 SCIENCE AS A NORMAL CHARACTER 497 00:32:22,666 --> 00:32:24,799 AND NOT ENDING OUR QUERY STRING. 498 00:32:24,800 --> 00:32:26,933 DOES I HAVE QUESTIONS ABOUT 499 00:32:26,933 --> 00:32:43,066 THIS? 500 00:32:43,066 --> 00:32:45,766 SORRY, NO QUESTIONS? 501 00:32:45,766 --> 00:32:46,066 OKAY. 502 00:32:46,066 --> 00:32:47,432 THEN WE'RE GOING TO MOVE ON TO 503 00:32:47,433 --> 00:32:55,799 OUR FIRST EXERCISE. 504 00:32:55,800 --> 00:32:57,033 ON THE SCREEN YOU'LL SEE THE 505 00:32:57,033 --> 00:32:59,433 QUESTIONS HOW MANY SPANISH 506 00:32:59,433 --> 00:33:01,499 ARTICLES ABOUT DIABETES ARE IN 507 00:33:01,500 --> 00:33:02,033 PUB MED. 508 00:33:02,033 --> 00:33:02,999 THERE'S A HINT THERE SO YOU 509 00:33:03,000 --> 00:33:04,566 DON'T HAVE TO LOOK UP THE TAGS. 510 00:33:04,566 --> 00:33:07,532 THAT'S THE LANGUAGE TAG USED. 511 00:33:07,533 --> 00:33:10,133 I WANT TO YOU DO THIS SEARCH IN 512 00:33:10,133 --> 00:33:10,933 E-DIRECT. 513 00:33:10,933 --> 00:33:12,433 YOU CAN VERIFY YOUR RESULTS IF 514 00:33:12,433 --> 00:33:24,799 YOU WANT TO IN PUB MED. 515 00:33:24,800 --> 00:33:25,900 IF YOU HAVE QUESTIONS WHILE 516 00:33:25,900 --> 00:33:28,433 YOU'RE WORKING ON IT FEEL FREE 517 00:33:28,433 --> 00:33:30,099 TO PUT THOSE INTO THE CHAT. 518 00:33:30,100 --> 00:33:32,800 I'LL CHECK IN IN ABOUT A MINUTE. 519 00:33:32,800 --> 00:33:33,200 520 00:33:33,200 --> 00:33:33,466 521 00:33:33,466 --> 00:33:36,999 GREAT. 522 00:33:37,000 --> 00:33:40,333 LOOKS LIKE WE'RE GETTING GREAT 523 00:33:40,333 --> 00:33:48,333 RESULTS. 524 00:33:48,333 --> 00:33:54,366 LET'S LOOK AT THE QUESTION. 525 00:33:54,366 --> 00:33:56,699 HOW MANY SPANISH LANGUAGE 526 00:33:56,700 --> 00:33:58,033 ARTICLES ABOUT DIABETES IN PUB 527 00:33:58,033 --> 00:33:58,466 MED. 528 00:33:58,466 --> 00:34:00,366 RIGHT AWAY WE KNOW WE'RE DOING A 529 00:34:00,366 --> 00:34:00,666 SEARCH. 530 00:34:00,666 --> 00:34:02,099 THE FIRST THING WE WANT TO DO IS 531 00:34:02,100 --> 00:34:03,233 ENTER OUR COMMAND WHICH IS 532 00:34:03,233 --> 00:34:04,499 E-SEARCH. 533 00:34:04,500 --> 00:34:15,166 AND WE'VE SAID AND PUB MED. 534 00:34:15,166 --> 00:34:17,399 THE NEXT ARGUMENT IS A QUERY. 535 00:34:17,400 --> 00:34:19,266 WE'RE LOOKING FOR ARTICLES ABOUT 536 00:34:19,266 --> 00:34:38,966 DIABETES. 537 00:34:38,966 --> 00:34:41,866 AND WE WANT TO LIMIT IT TO 538 00:34:41,866 --> 00:34:42,666 SPANISH ARTICLE. 539 00:34:42,666 --> 00:34:44,966 WE HAVE OUR COMMAND AND 540 00:34:44,966 --> 00:34:51,199 ARGUMENTS AGAINST THE COMMAND. 541 00:34:51,200 --> 00:34:54,566 AND MANY ARE CORRECT IT'S 3,865. 542 00:34:54,566 --> 00:34:56,532 IF WE WANTED TO VERIFY THIS IN 543 00:34:56,533 --> 00:35:14,499 PUB MED IT'S AS SIMPLE AS. 544 00:35:14,500 --> 00:35:17,733 THERE YOU SEE 3,865. 545 00:35:17,733 --> 00:35:38,466 I'LL JUMP INTO ANOTHER EXERCISE. 546 00:35:38,466 --> 00:35:41,199 HOW DO YOU CONDUCT AN AUTHOR 547 00:35:41,200 --> 00:35:42,566 SEARCH IN PUB MED. 548 00:35:42,566 --> 00:35:43,866 NEXT THING THERE'S TWO WAYS TO 549 00:35:43,866 --> 00:35:51,299 LIMIT YOUR SEARCH ON THE PDAT OR 550 00:35:51,300 --> 00:35:54,200 USE THE DATE TYPE ARGUMENT. 551 00:35:54,200 --> 00:35:56,000 GO AHEAD AND FORMULATE YOUR 552 00:35:56,000 --> 00:35:57,300 SOLUTION. 553 00:35:57,300 --> 00:36:00,133 WHEN YOU'RE DONE GO AHEAD AND IN 554 00:36:00,133 --> 00:36:01,899 THE CHAT BOX LET ME KNOW IF YOU 555 00:36:01,900 --> 00:36:07,300 USED -- YOU PUT IT IN YOUR QUERY 556 00:36:07,300 --> 00:36:08,600 ARGUMENT FOR THE DATE 557 00:36:08,600 --> 00:36:09,966 LIMITATIONS OR ACTUALLY USED THE 558 00:36:09,966 --> 00:36:10,766 ARGUMENT. 559 00:36:10,766 --> 00:36:12,366 THE DATE TYPE ARGUMENT. 560 00:36:12,366 --> 00:36:13,999 JUST PUT THAT IN YOUR CHAT 561 00:36:14,000 --> 00:36:15,633 RESULTS WHEN YOU'RE DONE AND 562 00:36:15,633 --> 00:36:17,266 I'LL GIVE YOU TWO MORE MINUTES 563 00:36:17,266 --> 00:36:22,066 TO GET THAT ONE DONE. 564 00:36:22,066 --> 00:36:28,032 THIS ONE WAS A LITTLE TRICKY, BECAUSE THERE WAS A COUPLE THINGS YOU NEEDED TO KNOW 565 00:36:28,033 --> 00:36:31,133 TO CONSTRUCT YOUR SEARCH 566 00:36:31,133 --> 00:36:35,733 I'M HERE AT MY E-DIRECT PROMPT 567 00:36:35,733 --> 00:36:37,166 AGAIN AND GOING TO CLEAR MY 568 00:36:37,166 --> 00:36:38,366 SCREEN. 569 00:36:38,366 --> 00:36:41,199 SO WE'RE LOOKING FOR HOW MANY 570 00:36:41,200 --> 00:36:43,866 ARTICLES WERE WRITTEN BY BH 571 00:36:43,866 --> 00:36:53,599 SMITH BETWEEN 2012 AND 2017 IN 572 00:36:53,600 --> 00:36:58,200 -- INCLUSIVELY. 573 00:36:58,200 --> 00:37:02,600 IT LOOKS LIKE MOST USE BIG TYPE 574 00:37:02,600 --> 00:37:04,800 PDAT SO I'LL USE THAT AS WELL 575 00:37:04,800 --> 00:37:05,966 WHEN I CONSTRUCT MY SEARCH. 576 00:37:05,966 --> 00:37:07,432 WE'LL START AT THE BEGINNING. 577 00:37:07,433 --> 00:37:08,833 OUR FIRST COMMAND WE'LL WANT 578 00:37:08,833 --> 00:37:10,833 WE'RE GOING A SEARCH OF PUB MED 579 00:37:10,833 --> 00:37:32,466 SO WE WILL START WITH E-SEARCH. 580 00:37:32,466 --> 00:37:33,899 -- ONE OF THE THINGS YOU NEED TO 581 00:37:33,900 --> 00:37:37,366 KNOW IS HOW TO BUILD AN AUTHOR 582 00:37:37,366 --> 00:37:38,632 SEARCH. 583 00:37:38,633 --> 00:37:39,833 AUTHOR NAMES AND INVESTIGATOR 584 00:37:39,833 --> 00:37:42,066 NAMES IN PUB MED ARE INDEXED 585 00:37:42,066 --> 00:37:45,432 FROM LAST NAME, SPACE, UP TO TWO 586 00:37:45,433 --> 00:37:45,766 INITIALS. 587 00:37:45,766 --> 00:37:47,699 SO IF YOU WANT TO BE MOST 588 00:37:47,700 --> 00:37:49,233 EXACTING YOU'LL USE THE TWO 589 00:37:49,233 --> 00:37:51,666 INITIALS. 590 00:37:51,666 --> 00:37:54,366 WE HAVE THOSE SO I'LL TYPE IN 591 00:37:54,366 --> 00:37:56,166 SMITH BH AND GOING TO TAG THAT 592 00:37:56,166 --> 00:38:07,766 WITH THE AUTHOR TAG SINCE THAT'S 593 00:38:07,766 --> 00:38:11,466 WE WANT TO LIMIT IT FOR 594 00:38:11,466 --> 00:38:13,366 CITATIONS PUBLISHED BETWEEN 2012 595 00:38:13,366 --> 00:38:14,866 AND 2017. 596 00:38:14,866 --> 00:38:30,032 SO I NEED A DATE TYPE IT WILL BE 597 00:38:30,033 --> 00:38:32,999 A MINIMUM OF 2012 AND MAXIMUM 598 00:38:33,000 --> 00:38:47,866 DATE OF 2017. 599 00:38:47,866 --> 00:38:49,499 AND THIS IS A MISTAKE FOR THE 600 00:38:49,500 --> 00:38:52,900 DATE TYPE AND WE HAD THE 601 00:38:52,900 --> 00:38:54,000 CONVERSATION AND WE WERE ALL 602 00:38:54,000 --> 00:38:55,733 WRONG BECAUSE WE SAID IT COULD 603 00:38:55,733 --> 00:39:17,366 DEFAULT TO PDAT. 604 00:39:17,366 --> 00:39:19,499 IF WE DO THE SAME SEARCH IN PUB 605 00:39:19,500 --> 00:39:21,300 MED WE'RE LOOKING FOR SMITH BH 606 00:39:21,300 --> 00:39:43,433 AS THE AUTHOR AND CUSTOMIZE MY 607 00:39:43,433 --> 00:39:49,299 RANGE FROM 2012 TO 2017 FOR 127. 608 00:39:49,300 --> 00:39:49,900 SAME AMOUNT. 609 00:39:49,900 --> 00:39:50,866 I HAVE A MINUTE HERE. 610 00:39:50,866 --> 00:40:30,832 DO I HAVE QUESTION THAT ONE? 611 00:40:30,833 --> 00:40:33,066 ANYTHING WITH AN IDEA WHAT 612 00:40:33,066 --> 00:40:34,966 E-FETCH DOES. 613 00:40:34,966 --> 00:40:36,399 BLURT IT OUT OR TYPE IT. 614 00:40:36,400 --> 00:41:15,300 SO WHAT DOES E-FETCH DO? 615 00:41:15,300 --> 00:41:21,600 I LIKE ALLEN'S DEFINITION THE 616 00:41:21,600 --> 00:41:22,666 OTHERS ARE CLOSE BUT NOT 617 00:41:22,666 --> 00:41:24,699 COMPLETE BUT MAYBE GET TO THE 618 00:41:24,700 --> 00:41:30,266 HEART OF IT. 619 00:41:30,266 --> 00:41:32,066 IT RETRIEVES FULL REPORTS FROM 620 00:41:32,066 --> 00:41:35,899 PMIDs AND IN A VARIETY OF 621 00:41:35,900 --> 00:41:39,633 FORMATS. 622 00:41:39,633 --> 00:41:41,199 HERE'S GOING TO BE OUR FIRST 623 00:41:41,200 --> 00:41:58,600 EXAMPLE. 624 00:41:58,600 --> 00:41:59,966 WE WANT TO REVIEW THEM ON THE 625 00:41:59,966 --> 00:42:01,866 SCREEN ON WHATEVER FORMAT IS 626 00:42:01,866 --> 00:42:05,666 MOST ADVANTAGEOUS FOR US. 627 00:42:05,666 --> 00:42:07,199 WE START CONSTRUCTING THIS THE 628 00:42:07,200 --> 00:42:17,533 SAME WAY SO WE'RE SEARCHING FROM 629 00:42:17,533 --> 00:42:20,166 PUB SO WE WANT E-FETCH AS OUR 630 00:42:20,166 --> 00:42:21,499 COMMAND AND NEED TO BUILD THE 631 00:42:21,500 --> 00:42:23,233 ARGUMENTS INTO IT SO IT KNOWS 632 00:42:23,233 --> 00:42:24,466 WHAT WE'RE TRYING TO ACCOMPLISH. 633 00:42:24,466 --> 00:42:28,332 WE WANT TO QUERY -- WE WANT TO 634 00:42:28,333 --> 00:42:33,966 HIT THE DATABASE IN PUB MED SO 635 00:42:33,966 --> 00:42:41,399 WE SPECIFY THAT AND WANT A 636 00:42:41,400 --> 00:42:44,466 UNIQUE IDENTIFIER AND I'LL 637 00:42:44,466 --> 00:42:53,632 RETRIEVE THE PMID25359968. 638 00:42:53,633 --> 00:43:04,533 I NEED THAT IN THE FORMAT OF THE 639 00:43:04,533 --> 00:43:06,733 AC TRACT VIEW. 640 00:43:06,733 --> 00:43:11,199 THEN I HIT ENTER. 641 00:43:11,200 --> 00:43:12,700 WHAT YOU'RE SEEING ON YOUR 642 00:43:12,700 --> 00:43:14,800 SCREEN YOU'RE SEEING THE 643 00:43:14,800 --> 00:43:18,066 ABSTRACT VIEW OF A SINGLE 644 00:43:18,066 --> 00:43:18,432 CITATION. 645 00:43:18,433 --> 00:43:20,299 THE NAME, THE ARTICLE, THE 646 00:43:20,300 --> 00:43:21,533 JOURNAL IT CAME FROM THE 647 00:43:21,533 --> 00:43:24,133 AUTHOR'S LISTED THERE AND THE 648 00:43:24,133 --> 00:43:27,499 AFFILIATION DAUGHTER. 649 00:43:27,500 --> 00:43:34,466 -- DATA AND IDENTIFIERS FOR IT 650 00:43:34,466 --> 00:43:37,866 AND I.D. WITHIN PUB MED AND I.D. 651 00:43:37,866 --> 00:43:45,899 WITHIN PUB MED. 652 00:43:45,900 --> 00:43:48,433 YOU CAN GET THESE RECORDS IN A 653 00:43:48,433 --> 00:43:55,199 MULT TUESDAY OF FORMATS. 654 00:43:55,200 --> 00:43:58,766 WE JUST LOOKED AT THE ABSTRACT 655 00:43:58,766 --> 00:44:00,632 VIEW AND IF YOU USE PUB MED AT 656 00:44:00,633 --> 00:44:02,633 ALL YOU'LL NOTICE HERE ARE THE 657 00:44:02,633 --> 00:44:04,666 MED LIN TAGS AND THERE'S THE 658 00:44:04,666 --> 00:44:19,432 DATA FOR EACH. 659 00:44:19,433 --> 00:44:22,566 I'LL RETRIEVE THE SAME RECORD IN 660 00:44:22,566 --> 00:44:26,099 XML FORMAT AND YOU'LL SEE THE 661 00:44:26,100 --> 00:44:29,266 OPEN AND CLOSE TAGS AND THE 662 00:44:29,266 --> 00:44:30,566 ASSOCIATED DATA FOR EACH FIELD. 663 00:44:30,566 --> 00:44:32,999 YOU SEE THE DIFFERENT FORMATS 664 00:44:33,000 --> 00:44:35,200 HAVE DIFFERENT LENGTHS AND HOW 665 00:44:35,200 --> 00:44:37,566 EASY IT IS TO HUMAN VIEW THOSE. 666 00:44:37,566 --> 00:44:45,232 AND LASTLY I CAN RETRIEVE THIS 667 00:44:45,233 --> 00:44:47,566 AS A PMID. 668 00:44:47,566 --> 00:44:50,332 I'LL LET IT HANG WHY YOU'LL WANT 669 00:44:50,333 --> 00:44:52,333 TO DO THAT UNTIL THE FUTURE 670 00:44:52,333 --> 00:44:54,199 CLASSES SO YOU CAN SEE WHAT KIND 671 00:44:54,200 --> 00:44:56,833 OF CASE YOU'LL NEED THAT FOR. 672 00:44:56,833 --> 00:45:00,433 THE FORMATS YOU CAN RETRIEVE ARE 673 00:45:00,433 --> 00:45:02,866 DEPENDENT ON THE DATABASE YOU'RE 674 00:45:02,866 --> 00:45:03,332 QUERYING. 675 00:45:03,333 --> 00:45:07,366 I RAN A FEW OF THEM DEPENDING ON 676 00:45:07,366 --> 00:45:09,799 THE DATABASE YOU'RE USING SO AN 677 00:45:09,800 --> 00:45:11,233 BE ATTRACT VIEW OF A GENE RECORD 678 00:45:11,233 --> 00:45:12,833 MAY OR MAY NOT MAKE SENSE. 679 00:45:12,833 --> 00:45:15,199 YOU CAN REVIEW THE DOCUMENTATION 680 00:45:15,200 --> 00:45:17,633 AND SEE WHAT FORMATS ARE 681 00:45:17,633 --> 00:45:18,733 AVAILABLE DEPENDING ON THE 682 00:45:18,733 --> 00:45:20,233 DATABASE YOU'RE USING. 683 00:45:20,233 --> 00:45:23,633 E-FETCH CAN ALSO RETRIEVE 684 00:45:23,633 --> 00:45:25,133 MULTIPLE RECORDS AT THE SAME 685 00:45:25,133 --> 00:45:31,533 TIME. 686 00:45:31,533 --> 00:45:33,099 FOR MY EXAMPLE AND I'M GOING TO 687 00:45:33,100 --> 00:45:34,933 CUT AND PASTE AND SEND BECAUSE 688 00:45:34,933 --> 00:45:43,299 I'LL HAVE MULTIPLE PMIDs OR UIDs 689 00:45:43,300 --> 00:45:45,700 AND YOU'LL SEE THAT'S BEEN 690 00:45:45,700 --> 00:45:59,233 OCCASIONALLY PROBLEMATIC. 691 00:45:59,233 --> 00:46:01,266 AND THERE'S THREE SEPARATED BY A 692 00:46:01,266 --> 00:46:10,566 COMMA. 693 00:46:10,566 --> 00:46:15,132 GO TO PMID1 AND HERE IN THE 694 00:46:15,133 --> 00:46:16,199 ABSTRACT YOU CAN CHANGE THE VIEW 695 00:46:16,200 --> 00:46:23,333 TO ANY YOU WANT. 696 00:46:23,333 --> 00:46:24,933 AS A WORD OF CAUTION USING 697 00:46:24,933 --> 00:46:26,933 E-FETCH YOU'RE RETRIEVING THE 698 00:46:26,933 --> 00:46:28,166 COMPLETE VIEW OF THE RECORD WHEN 699 00:46:28,166 --> 00:46:40,332 YOU GET IT AND SOMETIMES YOU CAN 700 00:46:40,333 --> 00:46:42,066 GET MORE THAN YOU ANTICIPATED. 701 00:46:42,066 --> 00:46:53,199 HERE'S A RECORD MIKE FOUND 702 00:46:53,200 --> 00:46:55,166 YOU'LL NOTICE IT TAKES UP SPACE 703 00:46:55,166 --> 00:46:56,232 ON THE SCREEN AND IS DIFFICULT 704 00:46:56,233 --> 00:47:04,799 TO VIEW IT HAS AUTHORS 705 00:47:04,800 --> 00:47:05,500 ASSOCIATED WITH IT. 706 00:47:05,500 --> 00:47:07,833 IF YOU EXTRAPOLATE THAT AND 707 00:47:07,833 --> 00:47:09,666 THINK YOU DID A SEARCH TO MAYBE 708 00:47:09,666 --> 00:47:19,832 100 PMIDs HOW UNUSABLE THE DATA 709 00:47:19,833 --> 00:47:23,366 ENDS UP BEING AND IT'S ANALYZING 710 00:47:23,366 --> 00:47:24,899 THE RESULTS BEFORE MOVING 711 00:47:24,900 --> 00:47:28,633 FORWARD. 712 00:47:28,633 --> 00:47:37,366 I'M GOING CLEAR MY SCREEN. 713 00:47:37,366 --> 00:47:40,732 AND AN EXERCISE ON E-FETCH. 714 00:47:40,733 --> 00:47:43,066 IT'S A SIMPLE ONE. 715 00:47:43,066 --> 00:47:46,632 WHO IS THE FIRST AUTHOR LISTED 716 00:47:46,633 --> 00:47:48,599 ON THE PUB MED RECORD AND SARA 717 00:47:48,600 --> 00:47:51,066 WILL PUT THAT PMID IN THE CHAT 718 00:47:51,066 --> 00:47:57,899 SO YOU CAN GRAB IT IF NECESSARY. 719 00:47:57,900 --> 00:48:00,033 THERE'S A FEW WAYS TO GET THIS. 720 00:48:00,033 --> 00:48:01,099 OBVIOUSLY I'M ASKING YOU TO VIEW 721 00:48:01,100 --> 00:48:02,200 THE RECORD. 722 00:48:02,200 --> 00:48:03,933 SO WHATEVER FORMAT YOU'RE 723 00:48:03,933 --> 00:48:05,799 COMFORTABLE IN DOING IT IN. 724 00:48:05,800 --> 00:48:06,866 I'LL GIVE YOU TWO MINUTES TO DO 725 00:48:06,866 --> 00:48:10,199 IT AND WE'LL GO OVER IT TOGETHER 726 00:48:10,200 --> 00:48:12,333 AGAIN. 727 00:48:12,333 --> 00:48:18,799 OKAY, LET'S GO OVER THIS ONE TOGETHER. 728 00:48:18,800 --> 00:48:22,166 I'M GOING TO GO INTO MY EDIRECT PROMPT 729 00:48:22,166 --> 00:48:24,432 AND GOING TO GRAB THE 730 00:48:24,433 --> 00:48:26,933 RECORD AND PMID LISTED THERE AND 731 00:48:26,933 --> 00:48:28,699 VIEW IT AND SEE WHO IS THE 732 00:48:28,700 --> 00:48:36,533 AUTHOR. 733 00:48:36,533 --> 00:48:37,833 YOU WANT TO GET THAT RECORD SO 734 00:48:37,833 --> 00:48:39,033 OUR FIRST COMMAND WILL BE 735 00:48:39,033 --> 00:48:42,166 E-FETCH BECAUSE WE WANT TO GRAB 736 00:48:42,166 --> 00:48:43,032 IT. 737 00:48:43,033 --> 00:48:44,466 YOU NEED TO TELL IT WITH YOUR 738 00:48:44,466 --> 00:48:46,032 FIRST ARGUMENT WHAT DATABASE 739 00:48:46,033 --> 00:48:48,766 WE'RE USING WHICH IS PUB MED AS 740 00:48:48,766 --> 00:48:54,799 IT HAS BEEN. 741 00:48:54,800 --> 00:48:57,366 SINCE WE'RE IN PUB MED THAT IS A 742 00:48:57,366 --> 00:48:58,832 PMID. 743 00:48:58,833 --> 00:49:19,099 WE'RE LOOKING FOR 26287646. 744 00:49:19,100 --> 00:49:21,400 YOU GO OVER HERE AND SEE THE 745 00:49:21,400 --> 00:49:22,433 AUTHOR LISTED. 746 00:49:22,433 --> 00:49:33,166 DR. BRENNON. 747 00:49:33,166 --> 00:49:39,366 MANY MANY LEVELS UP. 748 00:49:39,366 --> 00:49:40,966 SO IF YOU'RE STILL WORKING ON 749 00:49:40,966 --> 00:49:43,599 THE EXERCISE I'LL ASK YOU TO 750 00:49:43,600 --> 00:49:45,300 STOP AND WE'LL SHIFT GEARS AND I 751 00:49:45,300 --> 00:49:54,200 WANT TO TALK ABOUT CREATING A 752 00:49:54,200 --> 00:49:55,166 DATA PIPELINE. 753 00:49:55,166 --> 00:49:57,232 WHAT I SAID WHAT MAKES IT AN 754 00:49:57,233 --> 00:49:59,633 EFFICIENT TOOL IS USING COMMANDS 755 00:49:59,633 --> 00:50:01,433 USING ONE AS AN INPUT FOR 756 00:50:01,433 --> 00:50:03,699 ANOTHER. 757 00:50:03,700 --> 00:50:07,100 WE'RE CREATING A PIPELINE OF 758 00:50:07,100 --> 00:50:08,666 DATA THROUGH COMMANDS USING THE 759 00:50:08,666 --> 00:50:10,599 PIPE CHARACTER I HAVE SPOKEN 760 00:50:10,600 --> 00:50:11,466 ABOUT EARLIER. 761 00:50:11,466 --> 00:50:22,266 RIGHT NOW WE'VE TALKED ABOUT E 762 00:50:22,266 --> 00:50:24,999 SEARCH AND IF WE PUT IT FROM 763 00:50:25,000 --> 00:50:27,433 E-SEARCH TO E-FETCH WE GET THE 764 00:50:27,433 --> 00:50:32,566 RESULTS AS A LISTED PMIDs IN 765 00:50:32,566 --> 00:50:36,432 EXTRACT FORMAT OR ANY FORMATS WE 766 00:50:36,433 --> 00:50:37,233 WON OVER. 767 00:50:37,233 --> 00:50:38,399 USING THE PIPE COMMAND IS 768 00:50:38,400 --> 00:50:38,766 SIMPLE. 769 00:50:38,766 --> 00:50:41,199 YOU TYPE THE FIRST COMMAND. 770 00:50:41,200 --> 00:50:43,166 THE COMPLETE SEARCH COMMAND 771 00:50:43,166 --> 00:50:45,799 WE'RE DOING FOR AND TYPE A 772 00:50:45,800 --> 00:50:46,300 SPACE. 773 00:50:46,300 --> 00:50:48,866 TYPE IN THE PIPE CHARACTER AND 774 00:50:48,866 --> 00:50:50,366 SPACE AND YOU KEEP TYPING IN 775 00:50:50,366 --> 00:51:09,632 YOUR COMMAND. 776 00:51:09,633 --> 00:51:11,733 THIS WILL DEMONSTRATE CREATING A 777 00:51:11,733 --> 00:51:13,533 SEARCH THAT THEN FEEDS IN THE 778 00:51:13,533 --> 00:51:15,066 RETRIEVAL OF THAT ACTUAL 779 00:51:15,066 --> 00:51:15,399 DOCUMENT. 780 00:51:15,400 --> 00:51:24,300 SO I'M GOING CLEAR MY SCREEN. 781 00:51:24,300 --> 00:51:26,366 YOU WOULD DO COPYING AND PASTING 782 00:51:26,366 --> 00:51:27,332 FROM A NOTE FILE. 783 00:51:27,333 --> 00:51:55,966 I THINK KAREN BROUGHT IN THAT. 784 00:51:55,966 --> 00:51:57,466 I'M DOING A SEARCH OF PUB MED 785 00:51:57,466 --> 00:52:00,499 AND LOOKING FOR CITATIONS WITH A 786 00:52:00,500 --> 00:52:06,100 MAJOR HEADING OF ESPINOPIA AND 787 00:52:06,100 --> 00:52:08,933 THE SUBHEADING OF NURSING. 788 00:52:08,933 --> 00:52:11,233 SO THERE'S MY SEARCH COMMAND AND 789 00:52:11,233 --> 00:52:21,433 I WANT TO PIPE THIS. 790 00:52:21,433 --> 00:52:30,533 I PUT IN THE TYPE CHARACTER 791 00:52:30,533 --> 00:52:49,766 E-FETCH. 792 00:52:49,766 --> 00:52:52,166 I PUT IN FORMAT AND FOR MINE PUT 793 00:52:52,166 --> 00:52:55,932 IN THE PMIDs I'LL PUT IN THE 794 00:52:55,933 --> 00:52:56,466 DATABASE. 795 00:52:56,466 --> 00:52:59,666 WE'RE QUERYING PUB MED SO WE'RE 796 00:52:59,666 --> 00:53:09,799 RETRIEVING PMIDs. 797 00:53:09,800 --> 00:53:12,166 THEY'RE IN MY PMID FORMAT. 798 00:53:12,166 --> 00:53:14,632 I CAN CHANGE IT TO ABSTRACT AND 799 00:53:14,633 --> 00:53:16,233 RETRIEVE THE SAME THREE RECORDS 800 00:53:16,233 --> 00:53:20,466 AND VIEW THEM IN ABSTRACT MODE. 801 00:53:20,466 --> 00:53:22,332 SOMETIMES THESE LINES GET A BIT 802 00:53:22,333 --> 00:53:22,666 LONG. 803 00:53:22,666 --> 00:53:24,366 YOU CAN BREAK THEM UP AS YOU 804 00:53:24,366 --> 00:53:26,099 SAID BEFORE USING THE BACKSLASH. 805 00:53:26,100 --> 00:53:29,600 THAT MAKES IT MORE HUMAN 806 00:53:29,600 --> 00:53:32,266 READABLE FOR YOU TO PROOF YOUR 807 00:53:32,266 --> 00:53:49,632 SCRIPT BEFORE RUNNING THEM. 808 00:53:49,633 --> 00:53:52,333 SO WE'RE ABOUT TO DO AN EXERCISE 809 00:53:52,333 --> 00:53:56,299 WHERE WE RUN OUR FIRST 810 00:53:56,300 --> 00:53:59,200 MULTI-COMMAND SCRIPT. 811 00:53:59,200 --> 00:54:01,200 THINGS CAN GET UNWIELDY QUICKLY. 812 00:54:01,200 --> 00:54:07,233 YOU WANT TO KEEP YOUR QUERY 813 00:54:07,233 --> 00:54:07,699 MANAGEABLE. 814 00:54:07,700 --> 00:54:09,233 IT WON'T BE A LARGE SCRIPT BUT 815 00:54:09,233 --> 00:54:11,299 YOU'LL WANT TO REVIEW IT AND 816 00:54:11,300 --> 00:54:13,733 COMBINE COMMANDS SLOWLY AND KEEP 817 00:54:13,733 --> 00:54:16,466 THE COMMAND SET MANAGEABLE AND 818 00:54:16,466 --> 00:54:18,832 LASTLY WORK IN SMALL STEPS AND 819 00:54:18,833 --> 00:54:20,033 BUILD UP SLOWLY. 820 00:54:20,033 --> 00:54:21,866 SO FOR OUR FINAL EXERCISE WE'RE 821 00:54:21,866 --> 00:54:24,032 GOING TO WORK ON COMBINING 822 00:54:24,033 --> 00:54:25,566 COMMANDS. 823 00:54:25,566 --> 00:54:27,332 HOW DO WE GET A LIST OF ALL THE 824 00:54:27,333 --> 00:54:29,866 PMIDs FOR ALL THE ARTICLES 825 00:54:29,866 --> 00:54:35,166 WRITTEN BY BH SMITH BETWEEN 2012 826 00:54:35,166 --> 00:54:36,366 AND 2017. 827 00:54:36,366 --> 00:54:38,232 YOU'LL SEE IT BUILDS ON THE 828 00:54:38,233 --> 00:54:39,466 SEARCHS YOU'VE ALREADY 829 00:54:39,466 --> 00:54:39,966 CONDUCTED. 830 00:54:39,966 --> 00:54:41,466 WHILE YOU CAN SIT THERE AND 831 00:54:41,466 --> 00:54:43,466 RETYPE THEM YOU ALSO WANT TO 832 00:54:43,466 --> 00:54:44,632 THINK ABOUT USING THE UP AND 833 00:54:44,633 --> 00:54:46,866 DOWN ARROW KEYS TO GO THROUGH 834 00:54:46,866 --> 00:54:48,232 YOUR PREVIOUS COMMANDS OF 835 00:54:48,233 --> 00:54:49,366 SEARCHING YOU KNOW WORK WHICH 836 00:54:49,366 --> 00:54:54,766 FEEDS INTO MY SCRIPTS OF TESTING 837 00:54:54,766 --> 00:54:55,766 AND WORKING SLOWLY. 838 00:54:55,766 --> 00:54:57,099 ANOTHER HINT, WE'RE TRYING TO 839 00:54:57,100 --> 00:54:59,233 JUST GET THE PMIDs. 840 00:54:59,233 --> 00:55:00,533 THINK OF THE FORMAT YOU'RE 841 00:55:00,533 --> 00:55:01,833 TRYING TO GRAB THOSE IN AFTER 842 00:55:01,833 --> 00:55:05,266 YOU GOT THE QUERY BELT. 843 00:55:05,266 --> 00:55:07,299 I'LL GIVE YOU TWO TO THREE 844 00:55:07,300 --> 00:55:09,166 MINUTES TO WORK ON THIS. 845 00:55:09,166 --> 00:55:11,366 I UNDERSTAND IT'S LONGER. 846 00:55:11,366 --> 00:55:12,799 KNOW NEED TO POST YOUR RESULTS 847 00:55:12,800 --> 00:55:14,466 THIS TIME. 848 00:55:14,466 --> 00:55:16,032 WHAT YOU CAN DO IS GIVE ME A 849 00:55:16,033 --> 00:55:18,999 GREEN CHECK IN THE PARTICIPANTS 850 00:55:19,000 --> 00:55:20,600 PANEL WHEN YOU ARE DONE AND 851 00:55:20,600 --> 00:55:21,933 WE'LL GO EVER OUT TOGETHER. 852 00:55:21,933 --> 00:55:23,166 AGAIN, I'LL GIVE YOU ABOUT THREE 853 00:55:23,166 --> 00:55:25,199 MINUTES TO COMPLETE IT AND AS 854 00:55:25,200 --> 00:55:26,200 ALWAYS IF YOU HAVE ANY 855 00:55:26,200 --> 00:55:27,866 QUESTIONS, GO AHEAD AND AS YOU 856 00:55:27,866 --> 00:55:29,866 GO JUST PUT THEM IN THE CHAT 857 00:55:29,866 --> 00:55:31,866 PANEL OR YOU CAN UNMUTE OR JUST 858 00:55:31,866 --> 00:55:34,499 CALL THEM OUT. 859 00:55:34,500 --> 00:55:35,866 OKAY, GO AHEAD AND STOP, 860 00:55:35,866 --> 00:55:41,866 AND WE'RE GOING TO WORK ON THIS TOGETHER. SO WE'RE TRYING TO GET A LIST OF 861 00:55:41,866 --> 00:55:52,499 PMIDS FOR ALL OF THE CITATIONS FOR THE AUTHOR "SMITH BH" BETWEEN THE YEARS 2012 AND 2017, INCLUSIVE. 862 00:55:52,500 --> 00:55:56,200 THE FIRST THING I NEED TO DO, IS BUILD MY SEARCH 863 00:55:56,200 --> 00:55:58,833 SO MY FIRST COMMAND WOULD BE 864 00:55:58,833 --> 00:56:04,099 ESEARCH. I NEED TO SPECIFY MY DATABASE AGAIN. AND THEN, I WANT TO PUT 865 00:56:04,100 --> 00:56:07,866 MY ARGUMENT IN FOR MY QUERY, WHICH WE'VE SAID 866 00:56:07,866 --> 00:56:09,766 WE WANT TO LIMIT THAT TO 867 00:56:09,766 --> 00:56:13,366 ARTICLES FROM THE AUTHOR "SMITH BH" 868 00:56:13,366 --> 00:56:21,899 I NEED TO TAG THAT WITH MY [AUTHOR] 869 00:56:21,900 --> 00:56:27,766 AND WE WANT TO LIMIT THAT BETWEEN THE DATES. NOW I'VE USED THAT 870 00:56:27,766 --> 00:56:34,199 DATETYPE ARGUMENT QUITE A BIT, SO I'M GOING TO PUT THIS INTO MY SEARCH, 871 00:56:34,200 --> 00:56:43,433 AND I'M LOOKING FOR ARTICLES BETWEEN 2012 AND 872 00:56:43,433 --> 00:56:50,099 I NEED TO TAG THAT WITH [PDAT], AND I WANT THAT TO BE INCLUSIVE OF 873 00:56:50,100 --> 00:56:56,166 THE YEAR 2017 AS WELL. AND I NEED TO TAKE THAT TO THE END 874 00:56:56,166 --> 00:56:59,299 OF THE YEAR AND TAG IT, AND THEN CLOSE 875 00:56:59,300 --> 00:57:01,233 MY QUERY. 876 00:57:01,233 --> 00:57:08,433 NOW, THE NEXT 877 00:57:08,433 --> 00:57:13,399 THING I NEED TO DO IS, I WANT TO RETRIEVE THOSE PMIDS, 878 00:57:13,400 --> 00:57:19,433 SO I WANT TO FETCH THOSE ACTUAL RECORDS, AND I NEED TO PIPE THIS SEARCH 879 00:57:19,433 --> 00:57:22,633 OVER TO A COMMAND THAT CAN DO THAT. 880 00:57:22,633 --> 00:57:27,199 I'VE SAID THAT THE DATABASE PIPES WITH IT, SO THERE'S NO NEED TO REALLY SPECIFY THAT, 881 00:57:27,200 --> 00:57:30,533 BUT I DO NEED TO TELL IT WHAT FORMAT I WANT THESE RECORDS IN. 882 00:57:30,533 --> 00:57:35,233 AND I WANT THE UIDS OR THE PMIDS. 883 00:57:35,233 --> 00:57:45,966 THIS IS A LITTLE MORE INTENSIVE SEARCH. YOU SAW A TIME DELAY. I'M GOING TO GRAB ONE OF THESE 884 00:57:45,966 --> 00:57:49,499 AND I'M GOING TO GO INTO PUBMED 885 00:57:49,500 --> 00:57:55,800 AND I'M JUST GOING TO PUNCH THIS UID, THIS PMID IN HERE, BRING UP THE RECORD. HERE YOU'LL SEE THE AUTHOR 886 00:57:55,800 --> 00:58:02,133 AND YOU'LL SEE THIS WAS PUBLISHED IN 2013 WHICH IS DEFINITELY INCLUSIVE OF OUR DATE RANGE. 887 00:58:02,133 --> 00:58:06,066 OKAY, WE'RE RUNNING OUT OF TIME. 888 00:58:06,066 --> 00:58:10,999 JUST HAVE A COUPLE LAST ITEMS TO GO OVER. 889 00:58:11,000 --> 00:58:12,600 SO THAT'S ABOUT IT FOR OUR TIME TODAY 890 00:58:12,600 --> 00:58:14,033 SO MAKE SURE YOU COME BACK ON 891 00:58:14,033 --> 00:58:16,066 THURSDAY SARA'S GOING TO TALK 892 00:58:16,066 --> 00:58:18,399 ABOUT HOW TO GET SPECIFIC DATA 893 00:58:18,400 --> 00:58:20,333 AND TABULATE THEM USING THE 894 00:58:20,333 --> 00:58:21,899 EXTRACT COMMAND. 895 00:58:21,900 --> 00:58:23,300 IN THE MEANTIME IF YOU'RE 896 00:58:23,300 --> 00:58:25,666 CURIOUS ABOUT UNIX OR WANT TO 897 00:58:25,666 --> 00:58:27,732 LEARN MORE I HAVE A LINK HERE ON 898 00:58:27,733 --> 00:58:28,266 THE SLIDE. 899 00:58:28,266 --> 00:58:30,532 THIS IS A GREAT NCBI ABOUT 900 00:58:30,533 --> 00:58:33,333 15-MINUTE WEBINAR OR GIVES YOU 901 00:58:33,333 --> 00:58:35,433 AN OVERVIEW OR REFRESHER IF 902 00:58:35,433 --> 00:58:37,366 YOU'RE FAMILIAR WITH UNIX AND 903 00:58:37,366 --> 00:58:39,799 GIVES YOU TIPS AND TRICKS. 904 00:58:39,800 --> 00:58:41,733 THIS IS A LINK TO THE USER'S 905 00:58:41,733 --> 00:58:42,799 GUIDE AND WHERE THE CLASS 906 00:58:42,800 --> 00:58:44,566 INFORMATION IS AND I'LL REVIEW 907 00:58:44,566 --> 00:58:48,166 THAT IN A SECOND. 908 00:58:48,166 --> 00:58:49,999 YOU CAN GET TO OUR CONTACT US 909 00:58:50,000 --> 00:58:51,433 AND WE'LL DO OUR BEST TO CONTACT 910 00:58:51,433 --> 00:58:52,899 YOU BEFORE THE NEXT CLASS. 911 00:58:52,900 --> 00:58:55,900 YOU CAN ALSO USE THE CONTACT US 912 00:58:55,900 --> 00:58:58,700 BUTTON ON THE USER'S GUIDE WEB 913 00:58:58,700 --> 00:58:59,866 PAGE. 914 00:58:59,866 --> 00:59:08,132 HERE'S THE WEB PAGE AND 915 00:59:08,133 --> 00:59:09,666 INSTRUCTIONS AND IN EDIRECT FOR 916 00:59:09,666 --> 00:59:12,466 PUB MED. 917 00:59:12,466 --> 00:59:14,699 WE'RE RUNNING LOW ON TIME. 918 00:59:14,700 --> 00:59:17,600 HERE'S THE CLASS MATERIALS. 919 00:59:17,600 --> 00:59:19,300 HERE'S THE HOMEWORK ON THE HONOR 920 00:59:19,300 --> 00:59:26,366 SYSTEM IS INCLUDED IN THE 921 00:59:26,366 --> 00:59:28,299 HANDOUT ON HOMEWORK FOR PART ONE 922 00:59:28,300 --> 00:59:29,633 AND IF YOU GET FRUSTRATED YOU 923 00:59:29,633 --> 00:59:31,233 CAN COME UNDER THE SAMPLE CODE 924 00:59:31,233 --> 00:59:33,766 FOR THE CLASS AND AT THE BOTTOM 925 00:59:33,766 --> 00:59:35,266 YOU'LL SEE THE HOMEWORK 926 00:59:35,266 --> 00:59:41,199 SOLUTIONS AS WELL. 927 00:59:41,200 --> 00:59:43,433 AS I SAID THE HOMEWORK IS IN THE 928 00:59:43,433 --> 00:59:44,933 HONOR SYSTEM BUT IT WILL 929 00:59:44,933 --> 00:59:46,866 REINFORCE THE CLASS AND GET YOU 930 00:59:46,866 --> 00:59:49,332 READY FOR SARA'S CLASS THURSDAY. 931 00:59:49,333 --> 00:59:50,933 IF YOU HAVE ANY QUESTIONS IN THE 932 00:59:50,933 --> 00:59:53,099 MEANTIME PLEASE, GO AHEAD AND 933 00:59:53,100 --> 00:59:55,300 HIT THE CONTACT US BUTTON AT THE 934 00:59:55,300 --> 00:59:56,866 TOP OF EVERY PAGE AS YOU SEE IT 935 00:59:56,866 --> 01:00:03,132 HERE AND WE'LL ANSWER YOU. 936 01:00:03,133 --> 01:00:04,099 THANK YOU AGAIN FOR JOINING US 937 01:00:04,100 --> 01:00:05,300 AND IT'S BEEN A GREAT SESSION. 938 01:00:05,300 --> 01:00:06,466 I LOOK FORWARD TO CONTINUING THE 939 01:00:06,466 --> 01:00:07,832 NEXT TWO WEEKS WITH YOU. 940 01:00:07,833 --> 01:00:08,833 THANKS.